These changes are always immediately updated in the "molden5.x.tar.Z"
source file, however the platform dependent executables in the
directory "/pub/molgraph/molden/bin" on the ftp site are not always
in tune with the latest changes, check the date on the executable.
------------------------------------------------------------------------
Thu Dec 20
molden5.9.2
- Corrected reading of .plt files created by open3dqsar.
The .plt files were checked with the maestro program,
that naturally supports these files.
- Improved capturing errors of missing programs when using open3dqsar.
- Updated assigning charges to the mol files from an .sdf file.
In turned out that the oxygen in an 6- or 5- membered ring were not
assigned a mol2 atom type. This in turn led to charges not being assigned.
Tue Dec 11
molden5.9.1
- Updated the NwChem interface via the ecce.out file.
The ecce.out of the Hydrogen/Carbon atoms are now working.
The orbitals look OK.
The orbitals of a z-matrix optimisation of a z-matrix with dummys
now look ok.
Reading the acce.out now also the beta orbitals are read and a beta
density matrix is created.
When editing a molin.nw, a new molin.nw file is written to /tmp
and copied to a newly created directory with the name supplied a jobname.
- the popup box with help on the z-matrix editor variable fields now
only pops up once. They were getting in the way of an unimpeded functioning
of the z-matrix.
- Adding a button to undo the last applied changes to the z-matrix.
Also added the possibility to cancel selection of atoms to be connected
the new line, by hitting the 'escape' key.
- Added a new button to the file selector window. Besided replace and add there
is now a additional button "show", which shows the text content of the
file.
- Added new functionality to the file selector:
a) Now the buttons "Home", "End" "Page Up" and "Page Down" are now
functional.
b) Also you can scroll through the window with scroll button of the mouse.
c) You can now hit for instance the "a" key and the window will show the
first file beginning with the letter "a".
d) The "return" button now also works as a selector of files.
- Finally got the full binary distribution for molden5.9 on ubuntu
to run all external programs (pharmer,obabel,open3dqsar:
molden5.9.full.ubuntu.64.tar.gz).
Wed Nov 21
- Discovered an error in submitting gaussian jobs.
Molden would crash in such a case.
This error has been there at least since version molden5.7 !
In addition the correct gaussian environment variable was not
passed onto the rungau subroutine.
Fixed it.
- also added processing for G16 subnission.
molden5.9
Tue Nov 1
- Added a molden interface to open3DQSAR
- Use environment variable OPEN3DQSAR_PATH to point to the directory
where the open3dqsar executable is located.
Proper operation of open3dqsar relies on the presence of openbabel,
so this has to be installed as well.
- You will find the new option "Opem3DQSAR" under the "Surfaces icon"
(the 7th icon from above middle column).
When clicked, this will pop up the QSAR interface window.
Here the minimum inputs are:
1) a .sdf file with the pre-aligned structures
(ligands or small molecules), you will find ref.sdf in the test directory,
and
2) a text file with activities of the structures in the .sdf file,
you will find activity.txt in the test directory.
Now you can click "Run" and a the display window will show:
1) the aligned structures from the .sdf file
2) and four surfaces:
green and yellow are associated with the van der Waals
light blue and red are associated with the electrostatic field
You can hit the "Show Log" button to display the output of open3dqsar.
the "Show File" window will pop up. You can select to see output of
open3dqsar commands with the "Go To ->" button.
The "Edit" button pops up the "open3dqsar edit commands" window, that
shows the list of commands being sent to open3dqsar. When you select
an entry from this list, the entry will be copied to the edit box.
You can use the cursor keys to edit the command. When save is clicked
the edited command is saved to the list of open3dqsar commands to be
executed when the "Run Commands" button is clicked.
- Added the -Y commandline flag, telling molden to use a different
form of fractional to cartesian conversion. One that is in line with
vmd.
molden5.8.2
Tue Aug 14
- Docking was introduced in molden5.8, but this code did not always
yield the same results on the docking tests in the test/dock directory.
This in contrast to results on my development machine.
molden5.8.2 fixes some of these issues.
molden5.8.1
Fri Aug 3
- Made some adjustments to the C code (xwin.c) to make it compile
better on MacOSX
Thu Jul 26
- This version of molden, the electron density files for proteins are
obtained from a different site. The old one: the Electron Density
Server in Sweden is being phased out. Now we have to obtain electron
density files from www.ebi.ac.uk/pdbe. However the old site used
amongst others the BRICK/OMAP format of density files. The new site uses
the CCP4 format of density files. These are stream files, generated
by C programs. Fortran 2003 can read stream files, but some older
versions of fortran can not (f77,g77). These version of compilers
will generate errors.
- Heikki Tuononen reported a bug in molden5.8 with writing xyz files from
the Z-matrix editor.
- Also on recommendation of Heikki Tuononen we incorporated tables of
bond radii based Pyykkö's and Atsumi's values.
http://www.chem.helsinki.fi/~pyykko/Radii09.pdf
Molden5.8
Wed May 23 2018
- Three main functionalities were added in the molden5.8 release:
- molecular docking
- the updating of the nwchem functionality
- the writing of lammps input files from an ambfor .xyz file
by the ambfor executable by usage of the -l keyword
Molecular Docking
The docking functionality is a hybrid scheme of the FlexX docking
and a force field (amber+gaff) optimisation.
The same scheme as meployed by FlexX was used to generate the placement
of the base fragment. So first distance tables are generated to store
all the distances between the interaction points in the protein.
The protein has to be supplied in a pdb format with hydrogens present.
Molden can be used to generate such a pdb file. For now, the orientation
of for example OH groups (Serine,Threonine,tyrosine) have to be predefined.
The user can define a sphere around a to be picked point, which encloses
all the interaction points which are relevant for the docking.
These interaction point can be either H(ydrogen Bond)_Acc(eptor),
H(ydrogen Bond)_Don(onor) or aromatic/ch(2,3). The user selected
amino acid residues are then assigned interaction points.
For each combination of interaction groups, distances are collected and
stored in a distance table.
Next a ligand must be supplied in ambfor .xyz format (molden own force
field format), also charges must have been assigned for proper force
field scoring.
Next interaction points are assigned to the ligand. From these interaction
triples are generated. This list of triples is searched against the distance
tables to find matching protein interaction triples,
these are called base fragment
For the ligand two to three interaction points are generate for each
OH group.
Initially the ligand is divident up into fragments. Fragments are typically
connected by single SP3-SP3 or SP2-SP3 bonds. These fragments are stored
internally by molden. This fragmentation is used to generate different
conformations of the ligand by rotating around the dihedral angles of the
single bonds separating the fragments. The bonds that are not strict
SP2-SP3 bonds are kept in order to carry out a complete scan of the energy
with respect to these dihedrals. For regular SP3-SP3 bonds the standard
angles of the staggered conformations of ethane are employed.
When the debug button is pressed in the "Docking Start" window a file
called "conformers.mol2" is written.
The orientation of the base fragment is very important for the following
steps in the docking procedure. That is why the base fragment placement is
optimised to obtain a near perfect placement. If we had a base fragment
consisting of all Hydrogen bond acceptors and donors, the van der waals
part of the force field scoring is reduced, so that the orientation is
dominated by electrostatic part of the force field scoring.
If we were dealing with a base fragment with one pair of Hydrogen bond
acceptors or donors and one hydrophobic interaction point, we rotate
around the axis formed by pair to find the energetically optimal angle for
the remaining hydrophobic interaction point with respect to the pair.
Because the hydrophobic interaction between hydrophobic interaction points
are much smaller than between a acceptor and donor pair (round about
seven times weaker) and are much less well defined in space, the optimal
placement is rarely the one found in the original base placement, but
will be impacted more by the rest of the ligands placement.
The main scheme assumes a base fragment that has
interaction points belonging to the same fragment. This is by far the
fastest docking scheme. Here we map the base fragment onto the earlier
created conformers (Debug: mconformers.mol2), followed by an optimisation
of the conformers along the dihedrals of the non-pure single bonds
that molden stored earlier.
However when a ligand triplet with two or more Hydrogen bond acceptor/donor
interaction points can not be formed from the same fragment, a different
docking scheme is employed. Now we use the whole of the conformations of the
ligand to sample ligand points, but to make the algoritm more efficient we
only keep the unique ones (unique by location of the interaction points
origin) and store the conformations it belongs to with these interaction
points. After optimisation of the base fragments, the ligand poses are
generated from the combined confomer information of the three interaction
points. If all three interaction points are from the same conformer,
this conformer is mapped onto the base fragment, followed by an optimisation
of the conformers along the dihedrals of the non-pure single bonds
that molden stored earlier.
The force field scoring is stored into the multi-mol result dock.mol2
file.
The source distribution of molden5.8 has a 'dock' subdirectory of the test
directory, with three different docking:
- ligand dtst.xyz (part of MTX) into the 4dfr protein.
(fastest: all three interaction points on the same fragment)
- ligand est.xyz into the 1a52 protein.
Slower because the default interaction point separation of 10 angstrom
has to be increased.
- ligand rsb.xyz (part of RAL(oxifen)) into the 1err protein.
(slowest: NOT all three interaction points on the same fragment)
This is the launching of a prototype that will undergo extensive testing
in the coming months.
CAVEATS/Missing functionality:
- the orientation of the for example OH groups (Serine,Threonine,tyrosine)
have to be predefined in the PDB file.
- Structural and Non-structural waters are ignored in the docking.
- Docking into an active site with metals is not yest supported.
- No ring conformations are being searched
Updated nwchem functionality
Molden NWCHEM functionality has been updated. Previous versions of
molden could not display orbitals or density from NWCHEM because the
required information was missing from the NWCHEM output. However
NWCHEM is bundled with the ecce program, this program can display
the orbitals and other properties by incorporating ecce_print
command into the nwchem input file. Molden can now also read these
ecce.out files. This opens up a lot of functionality compared to
that of only the nwchem output file information being available.
Some caveats:
The scf convergence information written to the ecce.out
is not correct. At least in the somewhat old combination
of ecce and nwchem we used (nwchem 6.3)
Molden can not correctly calculate esp charges when dummys
are being used
Beside the reading of ecce files, molden can now also submit nwchem jobs
via the z-matrix editor (use the NWCHEM button in the format section
followed by "Submit Job"). The command nwchem must be defined for this to
work correctly.
WRITING OF LAMMPS INPUT FILES
Large-scale Atomic/Molecular Massively Paralell Simulator (LAMMPS)
input files can be generated from an Ambfor .xyz file, by Molden
own force field helper programs ambfor by typing:
ambfor -s -l test.xyz
After this a file called 'gaff.lammps' will have been written.
MISCELLANEOUS
- The reading of molden format files (such as vib.molden) has been repaired
- When reading multi-mol file such as a .mol2 file contaning multiple
structures, followed by reading an other multi-mol file when still having
the multi-mol window open, would lead to adding the entries to the entries
already present from the previuos read. This has been fixed.
Wed May 17 2017
- This is mainly an update to deal with the in my view 'crazily' increased
strictness of the gcc 5.4 compiler. This compiler spews out a ridiculous
number of warning messages. To cope with this, proper function proto typing
was applied to xwin.c. (Language purists always give me the creeps !)
Molden5.7
- Gaussian 16 was not recognised, which led to improper processing
of Guassian16 output/log files. Updated rdgaus.f to deal with this.
Thu Jan 26 2017
- Adjusted the dropdown list to print " "Optimise Hydrogens"
- added new keywords to run molden with a command file:
keywrd: WRXYZ=1-12
0 xyz file
1 mol file
2 msf file
3 tinker xyz file
4 '' ''
5 pdb file
6 chemx format
7 msi format
8 molden format file
9 mol2 file
11 ambfor xyz file
12 mopac xyz input file
This command allows to read in any by molden supported formats and
write out the specified format in file 'mol.xyz'
Sample molden command file:
title line
file=any_input_file wrxyz=11
This will write a ambfor xyz file. As input you could specify a pdb file.
The ambfor xyz file, will have hydrogens added, incomplete residues
corrected and charges and hydrogens added to ligands and water molecules.
keyword: WRMOPXYZ
Write an mopxyz input file.
keyword: CHARGE=-1
Specifies a total charge for the molecule to be written in conjuction
with the WRXYZ keyword.
keyword: WRTAUTO=1-12
0 xyz file
1 mol file
2 msf file
3 tinker xyz file
4 '' ''
5 pdb file
6 chemx format
7 msi format
8 molden format file
9 mol2 file
11 ambfor xyz file
12 mopac xyz input file
Generates enol tautomers from keto forms and writes them as tau01.xyz,
tauto02.xyz etc.
QMPSA calculates the polar surface area
Wed Sep 23
- Robert Gyepes reported a bug that would ignore the fill setting
in the space filling (3D) orbitals rendering in the Xwindows mode.
Fixed this.
Tue Sep 15
- fixed a bug when adding hydrogens to HETATM residues from the PDB,
using the plush directory. The first atom in the HETATM residue in the
plush directory would have its hydrogens omitted.
Sat Sep 12
- fixed a bug that would not let you add characters to a string after
you did a backspace on the start of a string
Fri Sep 4
- repaired a minor bug that would not label Hetatm molecules correctly
when no water was present in the pdb file.
Wed Sep 2
- Now when a water box is added, water and added ions can be displayed
independendly from the "HetAtm" button.
- Names of HETATM molecules from pdb files are passed on to ambfor .xyz and
.arc files and are displayed at such after ready these .xyz files into
molden
Thu Aug 20
- Restored proper visualisation of water in the water box added.
- When creating a crystal from scratch., by first creating a molecule
with the z-matrix editor and the chosing "pack cell" from the "cell"
icon, chosing "edit cell parameters" (choose P-1). The second molecule
related by the inversion symmetry was not shown. Now it is.
Tue Jul 21
- when reading in a pdb file, followed by optimise hydrogen positions,
then starting a force field optimisation with water box, connections
of water would be wrong. Fixed!
Fri Jul 3
- removed a bug that corrupted shadows
- the thousends of water on an amb(for/md) xyz file, are now represented
as just one HOH in the HETATM drop down list.
Thu Jul 2
- removed an other bug from pdb file writing routine for non-pdb structures.
This bug would cause a non-pdb structure to write a pdb file with only
a HEADER line.
- When having added a water box and subsequent optimisation with ambfor,
the resulting _opt.xyz would crash ambfor when using it to do further
optimisations.
- When viewing a ambfor xyz file with a water box added, selecting "backbone"
the box would disappear and oddly only reappear when switching on the first
HETATM residue. Fixed.
Also the color of the box would change to the selected color for the first
HETATM residue.
Tue Jun 30
- When writing PDB files with labels from the original PDB file
this would lead to wrong element labels after z-matrix editing of the
structure. Now the PDB file writing routine no longer uses these labels
after the z-matrix editor was used.
- The newly introduced labels on a residue basis would run out of its array
bounds, especially when many waters were present, causing a segment
violation. Fixed.
Molden5.4
- beginning of June 2015: EBI changed their MSD web interface for
there PDBE interface. As a result, the CML files of HETATM molcules
in the PDB were no longer available.
I therefor decided to create a local repository for Molden to get
information on hydrogens to add on HETATM molecules.
Now a 'plush' directory containing this information is added.
- Added the possibility to clip surfaces. This is especialy interesting
for molecular surface of proteins.
After creating a molecular surface, you click the "palette icon' ->
surface -> clip
Molden5.3
Sat May 30
- After Copying a hetatm molecule to a separate structure:
and then saving as pdb file, produced a file containing only
the HEADER line: fixed
- The 'plotplane' keywords in the opengl version of molden (gmolden)
did not update the screen, giving the wrong impression that nothing had
happened. Now the screen does update after plotplane commands such as
PHASE.
- In pdb entry 1fj3, Zn has a spurious connection to a H2o, of which
only half bond (the zn part) is displayed, the O side is not visible
on "contact" of Zn. This is fixed, now also this water is displayed.
Fri May 22
- Sometime back I introduced adding an extra hydrogen on tertiary
nitrogens, when adding hydrogens to ligands. Now this will only be done
if the three connected atoms to nitrogen do not lie in a plane.
- Added the Label On/Off entry to the popup menu for residues and hetatm
molecules. This lets labels be switched on/off on a residue basis
rather than on the whole molecule.
Thu May 7
- Adjusted rotamer generation for the different form of Histidine
(HIE,HID and HIP).
May 1
- Added a alternative way to generate rotamers.
Previously rotamers could only be changed after generating a z-matrix
for a protein. This was because rotamers change was accomplised changing
certain dihedral angles in the protein z-matrix.
The alternative method, aligns the stored rotamers of a particular type
of residue to the actual residue in the protein. To be more precise, it
aligns the backbone atoms (Calpha, N, COO and Cbeta).
The rotamer editing features are now also available without a z-matrix
having been built.
As a side effect the option to edit residues have been moved down in
the small residue popup window.
- Aligning and Combining two protein strcutures, now conserves displayed
residues in the backbone mode.
- The option restore incomplete residues now also makes use of the new
rotamer generation scheme.
------------------------------------------------------------------------
Molden5.2.4
Wed Apr 15
- Changed a minor detail in the source code for surf, that stops it from
core dumping wtih the latest versions of Ubuntu.
Fri Mar 20
- added option to make complete the incomplete protein residues.
It is available from the 'H' icon -> Optimise H postions.
- Previous, adding atoms to one of the twenty known protein residues
in the z-matrix editor these atoms would be flagged "NewRes".
However this was coded in such a way that while changing a amino acid
for another one this was also done, which is not correct.
Secondly the string for water in the hetatm arrays was overwritten.
This has been solved. In addition instead of "NewRes" now a string like
"gly.mod" is used to denoted the added atoms.
Fri Mar 13
- With combine/Align structures, now a new structure is created,
leaving the two original structures alone.
- Increased the speed of the optimsing water subroutine substantially
Wed Mar 5
- When loading PDB files -> zmat editor -> out if zmat editor -> add H's to
HETATM molecule -> zmat editor: the residue variable where not updated and
actually displayed the wrong variable. Fixed !!
- when animating residue variables in the z-matrix, in backbone mode:
only the animating residue was displayed, the rest disappeared (only molden
,gmolden was OK). Fixed !!
- made changes to the makefile where it calls the makefile in the ambfor
directory: no longer are the FFLAGS and CFLAGS exported.
When they are exported, they can cause ambfor to thow a lot of NaN
(Not a Number: the computer words can not hold the unexceptionally
large or small values of the varaible).
Until this is completely solved, use a gradient norm not smaller than 0.03
Wed Mar 4
- when writing a pdb file from Molden, the orginal labels of the HETATM records
would not be written, causing the add Hydrogens to HETATM not to work with
the newly written file.
- In the case of a pdb file read into Molden and subsequently opening the
z-matrix editor a z-matrix is made for the protein. When after leaving the
z-matrix editor hydrogens are added to HETATM molecules (via clicking with
the second mouse button on the molecule on screen, and selecting
"add hydrogens"), a new z-matrix has to be created including these newly
added hydrogens. This fix creates a new z-matrix in such a case.
Fri Feb 27
- When doing a charge calculation on a hetatm (PDB) molecule, only
-3,-2,-1,0,1,2,3 were offered to pick from. Now the oprion "other" is added.
- In the "molden file select" window an extra button has been added "Search PDB"
Clicking it will bring up a window that lets you search the PDB for keywords.
For example "quorum sensing", a list of matching pdb codes will be displayed.
When a pdb code is clicked a few lines from the description are displayed.
When "Load PDB code" is clicked the pdb structure will be downloaded and
displayed.
- a few help strings have been added.
- In the z-matrix when you click a field with the second mouse button.
A popup window lets select "animate", which would subsequently animate the
result of variable being increased/decreased.
The new way will open a window in which the variable can be increase or
decreased by one frame as well as animated.
During that the window is displayed all other windows will become
unresponsive, except the main drawing window, in which you will still
be able to rotate/translate your molecule.
- When opening the z-matrix editor on a PDB file, adding hydrogens to
HETATM molecules would nolonger work after the mutation of a residue.
This has been fixed.
Wed Jan 28
- Molden text editing input handling routines have been updated.
They now support dynamic editing: each entry field upon activation
now shows a cursor to indicate its position. On that position you can now
type characters or delete characters. Whereas previously you could only
add or delete at the end of the string.
- make molden now works again (no more unsatisfied external reference ogsel)..
- fixed a small bug with the gif snapshot routine. The top line of the
gif image was black or had garbage.
Molden5.2.3
Mon Jan 19
- The optimise hydrogen functionality is now split into to separate parts
which can be switched on and off in a small window.
- GLN/ASN flips will now only be done on complete residues
- Molden now checks before adding hydrogens to residues if the hydrogen
positions is not taken by a bonded atom (covalently bound hetatm).
- NO Hydrogens are added any longer to PO4 groups from the hetatm section
of a PDB file.
- NO Hydrogens are added any longer to COO (carboxyl) groups from the
hetatm section of a PDB file.
Molden5.2.2
Fri Nov 28
- When aligning two molecules the center of rotation was akward; fixed it.
- Molden can now also read gaussian input files with cartesian geometry
specification
- Molden can now read in z-matrices with only two lines. Use commandline
flag -d to get old behaviour.
Molden5.2.1
Mon Nov 3 2014
- From the Molden interface you can now create .avi movies.
This functionality depend on a third party package avconv.
(on linux: sudo apt-get install libav-tools).
Screen snap shots are made with the .bmp format.
- Fixed bug it the saving bmp function. This bug would only show it self
if the screen width was bigger than the screen height.
- Mopac2012 aux files are now better supported.
In the submit mopac job window, the keyword AUX is added by default.
If you use an older version of mopac, you might want to remove this
keyword again. (see xwin.c look for 'AUX').
Added method PM7.
Molden5.2
Wed Oct 22 2014
- Molden can now calculate the Electron Localization Function (ELF).
- Molden can now write .WFN style of wavefunction files.
It does not work with the use of 5D or 7F functions.
- When using Molden with gamess-us input files that contain cartesian
coordinates, Molden now recognises the use of coordinates specified in
angstroms. So now the connectivity is correctly displayed in such cases.
- with commandlineflag -J [0,1,2] molden can now write other screen dump
formats than gif [0] such as rgb [1] and bmp [2]. Gif is the default.
The high definition formats rgb and bmp are specially useful for
creating movies, such as with the ffmpeg package:
ffmpeg -i mol%03d.bmp -target dvd -s 800x800 movie.avi
- rdbas previously standard read 3dgridfile.
Now it can read any file by spcifying it after the rdbas
command:
rdbas=anyfile
- Created two new commands to specify the upper and lower limits of the
electrostatic potential treated as polar. This is in aid of the
calculation of polar surface area. POLUP=value POLLOW=value
Example of a keyword file mapping an electrostatic potential grid (mapfil)
onto on electron density grid (rdbas):
title
FILE=boxazepam_631g.out RDBAS=d0.3dgrid
MAPFIL=m0.3dgrid POLLOW=-0.075 POLUP=0.100 SPACE=0.01
- Molden now has rudimentary support for Mopac2012 output.
Full support is provided through the auxilliary file (.aux) mopac
creates through the use of the keyword AUX.
Molden5.1
Wed Jan 22 2014
- Updated the ambfor and ambmd codes to run optimisations and MD
on proteins faster. This hold for the optimisations with cutoff
They now use the Damped Shifted Force protocol by Fennell
Gezelter. Also creation of a water box has been sped up.
Molden5.0.7
Fri Jan 10 2014
- Paul Fleurat-Lessard did an update of the molden routines reading
VASP POSCAR and XDATCAR files. This was necesary to support a newer
version of these files.
- added the keyword 'wrmolf' to ne used in the molden command file.
'wrmolf' triggers the writing of a molden format file 'mol.molf'
- update the opengl secundary structure renderings (gmolden) of protein
being edit in the z-matrix (and in animated variables). This is important
for the psi and psi angles. Now the changes in psi and psi angles are
immediately applied to the structures on screen.
- molden compiled with gfortran would sometimes crash on an unexpected
end of line. Fixed it.
- molden format files with multiple sets of coordinates would not be displayed
correctly.
- When reading ambfor .xyz files, molden would not set the internal
(molden) variable ipdbt() for C-Terminal OXT residues. This would lead
to a faulty .xyz file written by molden, for instance on subsequent use
of the original file to start further ambfor/ambmd calculations.
- When doing from molden a MD run in the background (with ambmd), the first
read in .xyz file (by tnkfst in runjob.f) would lose the reordering information
when more memory was allocated. This resulted strange water connectivity.
Fixed it.
Molden5.0.6
Tue Apr 9
- The functionality of adding hydrogens to hetatm residues was broken due to
change in the web service pdbechem. With this version it is again functional.
- gmolden: shader bug when using occlusion and Blur caused the screeen
to not be updated correctly on some systems.
- gmolden: Added a proper "balls & sticks" mode, next to the already existing
sticks mode (in gmolden incorrectly named as balls & sticks).
Molden5.0.5
Thu Dec 20
- Added to possibility to localize orbitals (boys scheme).
Next to the 'orbitals' button there is now a 'local' button.
Molden5.0.4
Mon Nov 26
- Added a ramachandran plot for proteins. It can be found as last option
under the 'Surface' icon.
- Fixed a bug that made the Average CH3 button disappear in the NMR spectrum.
Fri Nov 9
- Restructured file selection so that it can now be generally used.
Used the file selector in the "Read Grid" button in the density mode
and also on the "Vr" button where you can map an other grid onto the
first grid.
Added a filter to the file selector, nothing fancy just a substring match.
- Cleaned to code of molsint.f. Now when calculating distributed multipoles
Molden will report when mxsite is exceded. This usually only happens when
NO overlap contributions are shifted to atomic sites.
- Somebody reported problems on his self constructed gaussian style files.
Fixed this.
- Added a charges scaling option to ambfor (for example : ambfor -S 0.7)
- Ambfor will now parse a file called 'param' with alternative parameters
(If it exists of course).
Thu Sep 20
- Molden now by default no longer searches for mpi executables at start up.
On machines with terabytes of disks this can take very long.
- Updated reading of Orca files, so that geometry+gradient single point runs
should now also be supported.
Thu Sep 13
- Molden can now also read Gamess-US inputfiles with cartesian coordinates
- Adjusted the writing of ambfor .xyz files so that the file can still be
read by molden if there is an undefined atom type.
Fri Jul 13
- Molden used to read in the first point with orbitals for Gaussian09
This was because in the beginning of its release, the orbitals
of the stationary point were not printed.
Currently Gaussian09 does print the orbitals of the stationary point.
Now Molden will display the orbitals of the stationary point.
Fri Jun 15
- Molden now check then openGL vendor string to circumvent a bug
in the graphic drivers of intel video cards.
This caused a segment violation on _mesa_generate_mipmap
Thu Jun 7
- the .jdx file written with the use of the keyword PLECTRUM now
also contains information for use in combination with jspecview
and jmol.
Thu Apr 26
- included wrting of a .jdx file with the keyword PLECTRUM
- keyword SPACE=value now is honoured when reading cube/grid files
Thu Mar 15
- Made the generated web pages for spectra (keyword PLECTRUM) compatible
with Internet explorer.
Tue Feb 28
- Improved generation of the html page created with the use of the
PLECTRUM keyword. (see below Tue Feb 14).
The command used to convert the postscript file now is:
gs -sDEVICE=jpeggray -g1000x500 -dBATCH -dNOPAUSE -sOutputFile=spec.jpg spec.ps
The index.html file now also contains javascript code to view the
active normal mode as a red line drawn on the spectrum.
It also contains a table of available frequencies together with intensities,
they can be clicked.
Tue Feb 14
- The molden keyword PLECTRUM calculates a spectrum for files that have
frequency and intensity information, in addition it converts the
postscript file that contains the spectrum to a jpg file.
For the conversion to work the ghostscript program must be installed
and defined. The folowing command is used to generate spec.jpg:
gs -sDEVICE=jpeg -r500x250 -dBATCH -dNOPAUSE -sOutputFile=spec.jpg spec.ps
It also creates the files index.html, mol.xyz and freq???.xyz.
The last files contain animations of the normal modes. These can be used
for interactive spectra in combination with the jmol viewer.
- Rudimentary support for NWchem output files.
Mon Feb 13
- The xyz format already supported dummys with the 'xx' element label.
Now Banquo ('Bq') sites are also supported. Both are displayed with the 'xx'
label.
Fri Feb 02
- Added molden keywords SPECTRUM (and PLECTRUM) to calculate a spec.ps
from a molden commandfile. Only for files that have spectra information.
- Molden now visualizes a file with just one atom better.
Fri Jan 20
- Added keywords EXTPOSCHG and EXTNEGCHG which specify a single pointcharge
to be added for the calculating of the QM electrostatic potential.
This can be used to model a counter charge when calculating the Elec.
Pot. of an anion or cation.
EXTPOSCHG=(r.rr,r.rr,r.rr) where r.rr is a real number representing
the cartesian coordinates in Bohr.
- Added commandline flag -U to switch of using shaders. On some graphics
cards the opengl version (gmolden) can hang on setting up the shaders.
Mon Jan 9
- Some optimisation to shader code for the benefit of older graphics
cards under Ubuntu Natty
Sat Dec 31
- The lines representation of a surface in Opengl shader language
gave problems. Fixed it.
Thu Dec 1
- Molden uses the pdbechem service to find out what hydrogens to add
on ligands. Unfortunately, the URL for this service has changed.
I have updated Molden to point to the new URL.
Mon Nov 28
- Fixed blocky noise when using occlusion.
Mon Oct 24
- amfor xyz files with cell information were not correctly stored in
the internal common blocks of molden.
As a result writing a just optimised structure and comparing it with the
structure on screen would give different results.
Fixed it !
Sun Oct 23
- Reading molden format files that contain only data for MO coefficients
that are non-zero. When this file is not the first file read in
it could occur that coefficinet that should be zero were actually non-zero.
Fixed this.
Fri Oct 21
- Fixed small bug that would leave a atom selected in solid mode hovering
around when switched to line or stick mode.
- gmolden using shaders would sometimes not draw a surface as transparent
Mon Oct 17
- Added a bigger font for the labels of atoms and residues for the opengl
version gmolden.
Wed Oct 12
- added the commandline option '-k int' (int=0-15), to specify the
color used to plot lables. Only available for the openGL version (gmolden).
Thu Sep 29
- The by molden created *.ogl files can now also be read from the commandline:
./gmolden molden.ogl
Previously, these files could only be read from the filemanager.
Wed Sep 28
- fixed a bug that would leave the outvector of the plotplane essentially
as a nul vector. This would only occur if you let molden figure out
a default plane AND if the first three atoms would be on a line.
Fri Sep 23
- Built in a button to make a gif screen shot in the density mode.
- Pressing 'R' for shadows now does not make the background black when
no shader capability is found.
- when writing a ambfor .xyz file with crystal information, now also
expands the cell before writing.
Thu Sep 15
- GAFF atom type assignement: switched from default aromatic Nitrogen
type nb to nc. (nb is only for pure aromatic compounds such as pyridine)
- also truncated negative values (see Wed Sep 14).
Wed Sep 14
- fixed problem with writing cube files on 64-bits platforms.
Function values that are less than 1.0d-99, are 'truncated' to
1.0d-99
Mon Sep 5
- Fixed a bug in the C code that calls getpoi (Thanks to Ben Roberts,
University of Florida for fixing this). This bug could affect the
processing of Gaussian files.
- When there is only one (hetatm) molecule in a PDB file, molden would
not pass on the total charge to the routines that calculate partial charges,
even when it offered the possibility to set it. Fixed.
Thu Sep 1
- when the main window was resized (or -geom commandline option was used)
in the opengl version (gmolden), the rubber selection band for selecting
atoms in the z-matrix editor was wrongly displayed. This is now fixed.
- when assingning charges to hetatm molecules of pdb files, molden would
try to retrive the total the total charge from the pdbchem. If no valid
three letter residue identifier was defined it would return charge option
-15, as a result the default total charge in the "assign total charge"
window would be "quintet" in stead of "0". Such a situation would accur
when a ligand was added by combination of two structures in the structures
window.
Thu Aug 18
- When using xming as xwindows/opengl emulator, in the opengl mode when
using the "select by pointer" mode in the z-matrix editor, the rubberband
would not be drawn. This is now fixed.
Tue Aug 16
- When writing a Gamess-US style z-matrix and when variables were specified
as constants, Molden now writes an ifreez record and nzvar.
Wed Aug 10
- Added visualisation of calculated UV-spectra from TD-DFT calculations with
Gaussian. Please feel free to suggest improvements.
Mon Aug 8
- Fixed a bug which could make molden crash when having multiple structures.
- The output of the internally run 'locate' command on linux is now redirected
to /dev/null. So unsuspecting users are not confused.
- Added small tweaks to the gaff forcefield types assignment (nitrogen in
cyanide is now typed).
- Added a lot of ifdef statements to make sure older linux distributions
do not include the newer code for OpenGL shaders.
Mon Aug 1
- Fix for reading gaussian 09 output when coordinates were frozen.
Wed Jul 13
- reading of esp charges on gaussian output has now been put before reading of
basis-set. This way when no basis-set is written the esp charges
will still be read.
Mon Jul 4
- The 3D wireframe drawing (X-windows) of the density/orbital mesh was
no longer drawn with equal width and height when using the commandline
-geom 1600x800 qualifier (example). Fixed it.
The use of shadowmaps currently only works if you dont resize.
Thu Jun 30
- Introducing Shadow mapping, for proteins, the secondary structure cartoons
cast shadows on them selves. See the palette icon, option shadows.
Or just hit 'r' in the drawing screen.
Tue Jun 7
- Introduced a bug in reading multi xyz formats, some month ago. Fixed it.
Tue May 31
- There was a bug reading Mopac2009 output
Mon May 16
- Molden now prevents the jobname being the same as the file being currently
read. This can cause problems.
Wed May 12,13
- Removed a bugs from the mpi MD code.
Thu May 5
- gmolden will draw proteins faster in the space filling mode.
Wed May 4
- gmolden would be killed due to too much memory consumption, during an MD
run, fixed.
- xyz files containing more than 1000 structures, are now all accounted
for in the geom conv. window.
Thu Apr 28
- There is a bug detected in the fast water code of ambmd. I have
applied a temporary quick fix.
Tue Apr 12
- Added postprocessing options: Blur and Occlusion to the colorpalette
icon. These options work as toggles. It will slow this down a bit,
certainly on less powerfull systems (graphics card dependant).
This is only available if you run molden locally.
- Changed the default for gmolden (mixed openGL/Xwindows executable)
to be fullgl. You can still get the old mixed behaviour by using the
commandline option -F.
- Molden does now also better support the mol2 file dialect used by
the popular docking program FlexX.
- When calculating the contacts between a ligand and residues in opengl
mode, the distance labels where not correctly displayed at far away
distances. Fixed it.
Wed Apr 6
- input z-matrices having variable names longer than 8 characters were
not read in. I have now increased the maximum variable lenght to 10.
Wed Mar 16
- Molden now has per pixel lighting built in. This looks a lot better,
especially the specular lighting. The per pixel lighting is accomplished
with shaders. Windows emulators like Xming and Xwin32 do not support shaders,
so you will not see a difference there.
Mon Mar 14
- Molden compiled with gfortran had problems with reading the protein
density file, fixed it.
- Molden compiled with gfortran sometimes crashed when reading in a
second structure, fixed it.
Wed Mar 2
- Added a cutoff scheme for water-water interaction, see:
Is the Ewald summation still necessary? Pairwise alternatives to
the accepted standard for long-range electrostatics
Cristopher J. Fennell and J. Daniel Gezelter,
Journal of Chemical Physics. 124, 234104 (2006)
- Adapted the makefile to be a little more intelligent.
It now tries to figure out on what os it is. This will cover most
flavors of linux, MacOSX and cygwin.
Fri Feb 25
- Added support for the Gaussian 09, new IRC mode HPC.
By request of Prof. Ugo Cosentino
Thu Feb 17
- added a routine for water-water interections. It uses a lookup table.
It is unfortunately only a little bit faster (factor 0.66)
Fri Feb 11
- removed a bug that would not copy all of the force field information
after allocating memory for a water filled box.
Thu Feb 3
- Adding ions is now done depending on the electrostatic potential.
You can still invoke random placement with the commandline argument
-z on ambfor/ambmd (in combination with -b).
Wed Feb 2
- replaced use of fork by vfork in an attempt to stop forking errors
on windows7 (64bits version still has problems).
- When adding a water box in ambfor or ambmd automatically ions are
added to neutralise the box. The placement of the ions is accomplished
by replacing waters randomly
Fri Jan 28
- there is now also a multiprocessor version of the crystal optimiser.
- removed a small bug in the opengl version when reading a jaguar cube
file.
Tue Jan 25
- The molden/gmolden interface will now automatically detect whether the
openmpi executables have been built. If so an option to use multiple
processors will be availabe in the window that fires ambfor/ambmd jobs.
- Removed a bug in the multiprocessor version of the MD program, ambmd.
Each subprocess would have its own initial velocities, which in turn
would lead to different coordinates in each subprocess. Fixed it.
Thu Jan 13
- Finally got the interactive optimisation working flawless on
WindowsXP.
- Fixed continued rotation during interactive optimise.
- optimised update time during optimisations
Wed Jan 5
- Added atom type 'cz' to the GAFF force field, this is needed for guadinium
and arginine. Also added improper torsion to keep the C connected to the
three N's in one plane.
Tue Dec 7
- Crystal optimiser was only working for non-covalently bound crystals.
Current version has been tested on organic crystals and seems to work.
Molden5
- Added a crystal optimizer, based on the gaff force field.
Periodic conditions are enforced by translation symmetry copies.
NO ewald summations ! This is a beta test.
- Gamess-US irc data, bug fix. first atom was not displayed
- While adding support for the calculated NMR spectra, a bug was introduced
that made it impossible to set the maximum intensity in a spectrum.
fixed.
- When doing a combine structure on two proteins, the ligands are now also
colored by structure.
- When using combine + align on two none protein structures, the user
is asked to specify 3 pairs of atoms. Each pair consisting of one
atom from the first and one atom of the second molecule. The code
has been changed in such a way that only atoms can be selected
of the first/second structure.
- Adapted molden to be more vista/windows7 friendly.
- When aligning two structures no longer the pmf score window pops-up
after pressing escape two or more times.
- the interface to qchem and orca was only partly functional. Fixed it.
- The crystal information of a mol2 file was nolonger parsed, fixed it.
------------------------------------------------------------------------
Molden4.9
Wed Sep 22
- Updated molden to read gaussian09 IRC caclulations outputs.
Wed Aug 11
- Updated Updated reading of Gamess-us output, kindly supplied by
Mariusz Klobukowski. The number of electrons when using pseudopotentials
is also calculated correctly.
Mon Jun 21
- Updated reading of Gamess-us output, kindly supplied by Mariusz Klobukowski
1) to read results from hessian calculation in the latest version of
gamess-us (lines with mode symmetry information were added)
2) to read basis sets in semiempirical calculations (we changed gamess-us
to be able to see the semiempirical MOs, with the STO basis sets expanded
in terms of STO-nG expansions).
Thu Jun 17
- The reading of a gridkont file (Program GRID) has been moved from the
density mode to the molecular mode. Under the surface icon, there now is
an option "gridkont". The benefit of this move is visualisation of the
GRID molecular interaction together with the full opengl protein
visualisation and the use of clipping planes.
- added a box around the grid for gridkont and protein electron density.
Wed Jun 2
- Added the option to for the electron density to follow the current residue.
This build on a feature of molden to show the label of the residue
the pointer is currently over. In addition now also a block of
electron density follows the residue the pointer is currently over.
You can fix the postion of the block, by hitting the spacebar.
Hitting it again will make the block follow the pointer movement again.
This all in the context of the latest hanges to molden of Fri May 28.
See below.
Fri May 28
- Under the surface icon, there was the option electron density map.
Clicking this would try to read a file contaning protein electron
in the so called 'omap' or DSN6 format. These files are available
from the Electron Density Server at Uppsala University:
http://eds.bmc.uu.se/eds/
This functionality has been extended. When reading a pdb file the pdbid
is automatically parsed and stored. When clicking the "elec. Dens. Map'
option the pdbid is used to automatically retrieve the omap file from
the electron density server. (the program wget is used for this).
After the file is read, a window will pop up, where you can specify the
electron density contour level. The rendered electron density volume
can also be clipped in three directions, for clarity.
- on request from Paolo Tosco, molden4.9 now allows upto four keyword lines
in a molden keyword file.
Wed Apr 21
- When reading a protein ambfor .arc file, the secundury structure would be
all coils, fixed this.
Mon Apr 19
- When interactively omptimising a structure with a water box, molden
sometimes would not show the waters. Also aborting the optimisation
by pressing escape, would sometimes disrupt the X protocol.
Fixed.
- Updated the windows version.
Wed Apr 14
- When a ambfor xyz file was loaded after a pdb file, its secundary
would be all coils. Fixed.
Tue Apr 13
- When reading a ambfor xyz file, nolonger the hydrogen bonds are
calculated by default. In the presence of a big water box this becomes
very slow.
- Going into the zmatrix editor the waters were stored. After quitting
the zmatrix editor, the waters were restored. However in the presence
of a large water box, the restoration was very slow. Fixed.
- Using the default optimiser(lbfgs) now also the waters that water out
of the box are come in to the other side of the box.
Mon Apr 12
- When interactively optimising a small molecule , in the presence of
water box, the waters and box would not be visible in the line drawing
mode (solid was ok). Fixed.
The box itself is now also visible.
- In the residue command window, when multiple chains were available,
you would have to specify the chain also in order to visualise residues.
This is now changed. You can however still use the chain identifier:
*:A for example will switch on all residues belonging to the A chain.
- When reading an ambfor xyz file containing a protein, and subsequently
writing a PDB file, every first residue of a chain had residue number 1.
This caused probelms when there were chains consisting of 1 residue.
Such a pdb file would not parsew correctly. Now all residues have a unique
number.
- reading an ambfor xyz file with a box specified, would lead to an empty
screen when opening the z-matrix editor. This is fixed.
- When optimising the Hydrogen positions, waters that are close to a metal
center now also have hydrogens added.
- Water boxes containing more than 5000 waters would have a corrupt [RESIDUE]
section in the ambfor xyz file. This would lead to artifact in visiulisation
with molden.
Wed Apr 7
- ambfor: made ff99sb the default protein force field. The unmodified
amber 99 force field will be used when specifying the -x
commandline flag
- ambfor: for rna/dna modelling the ff99bsc0 modification of the amber
force field will be used when specifying the -y
commandline flag
- fixed a bug that would visually screw up the secundary structure, when
in the xwindow mode.
- in the standard molden xwindow version the residue popup windows,
would have options, when clicked would activate the wrong action.
This bug was introduced the week before.
Thu Apr 1
- absolute scores for histidines were still to big, relative scores
were already OK.
- fixed a bug is the secundary visualisation, which under very special
circumstances would not show part of the coil.
- The small amino acid menues you can bring up by clicking with the second
mouse button now also contain an option to change the protonation states
for histidine, and a flip option for asn and gln
- In ambfor the total charge on non amino acid residues is checked and
corrected if it does not add up to a discrete integer.
Thu Mar 25
- fixed a major bug in calculating the scores for histidine (D,E,+),
under the optimise hydrogen positions.
- added prediction of asn/gln flips, under the optimise hydrogen positions
Fri Mar 19
- Fixed a bug that could make the hetatm residues disappear in the z-matrix
editor, when previously "Opt H pos." was used.
- when aligning two protein structures, both structures have a different color.
Also in the backbone mode the secondary structure visualisation will have a
different color per structure.
- when combining two small molecules from the structure window, you will now
be asked to move the two structures into visible range.
- when using command from the residue command window in combination with
the SURF keyword, molden will now display opengl surfaces in opengl mode.
- cysteines missing an HG atom will now have partial charges adding up to -1.
This also implemented in ambfor.
- some pdb structures containing hydrogens with labels not recognised by
molden are now recognized. There are probably more, let me know
if you find more.
- fixed a bug that would make some surfaces not being displayed in the
surfaces window. This could also cause: surface OFF, not to work.
Mon Mar 8
- added ambfor support for modified nucleotides such as:
1MA,5MC,OMC,2MG,M2G,7MG,OMG,YG,H2U,5MU,PSU
NOT supported are:
1MG,I,+U
- water oxygen atoms connected to the protein are disconnected before
writing ambfor xyz files.
Wed Feb 24
- fixed a minor bug that would give a superposed atoms in z-matrix,
after doing optimise hydrogen positions on a dna molecule.
Tue Feb 23
- for rna to z-matrix molden now takes an OXT atom in to account.
Mon Feb 22
- Added parameters for nucleotides to the amber force field implementation
in molden and ambfor.
- corrected charges for water, which did not completely add up to zero.
Mon Feb 1
- G09 has different zmatrix output than G03. Molden can now deal with this.
Tue Jan 26
- Molden4.9 introduces to optimisation method lbfgs as default optimisation
algorithem for Ambfor. Together with some other code optimisations, this
increases the speed of ambfor with a factor 4.
- changed param.f, such that less continuation lines are used.
The many continuation lines caused problems with compilers such as ifort.
Wed Dec 23
- more bug fixes concerning interaction between Molden with Tinker and Ambfor.
Tue Dec 22
- MAJOR Bug fixes concerning interaction between Molden with Tinker and Ambfor.
For ambfor the bug was introduced on 27 November, when the writing of ambfor
xyz files was changed. This bug is now fixed.
Ambfor will now write a file 'ambfor.wr' to indicate it is writing
intermediate optimisation files, when done writing it will remove this
lock file. This improves the interaction with Molden, which in some cases
would begin to read the file when its writing was not yet complete, resulting
in incomplete structure on screen.
The interface with Tinker was compromised earlier when ambfor started to
write intermediate files in binary form. Tinker and Ambfor now have their
own reading routines.
The jobname.run file, a csh script now has a -f added to the #!/bin/csh
line. This is because .cshrc files could contain commands preventing the
succesful executing of this file.
An number of buttons not applicable to Tinker jobs are now nolonger visible
in the Tinker optimise window.
Sat Dec 19
- fixed a small bug that interfered with wget, which molden uses to
fetch pdb and hydrogen positions to add to ligands.
- fixed a bug that would make ambfor crash when using the -N option
in combination with a liagnd being present
Thu Dec 17
- The switching function for the electrostatic used with cutoff with ambfor
caused distortions of the final protein geometry. I switched to a
shifting function for the electrostatics to solve this problem.
- The use of switching/cutoffs (commandline flag -N) in ambfor/ambmd
is now twice as fast.
Mon Dec 14
- Open shell stuctures are now also read from a Mopac2007 .aux file.
- Molden now tries to find the environment variable g09root
- Fixed a small bug that could make Molden crash after reading in two
large structures.
- Fix that treats negative J-couplings correctly (NMR from gaussian)
Thu Dec 10
- In addition to 1H NMR, molden now also calculates the 13C NMR spectrum.
- The magnetic shielding and J-coupling corresponding with rotationally
equivalent Hydrogens can be averaged by clicking the corresponding
Button.
Wed Dec 9
- Molden can now display caculated H NMR spectra from gaussian
You need to have caculated magnetic shieldings and J-couplings
Mon Nov 30
- Fixed bug in reading nmr data from gaussian output.
Fri Nov 27
- Ambfor can now be run using cutoff's and switching functions: use the -N
commandline flag to use cutoffs and switching. This can be faster than
all atom optimisation ( a lot).
The window form which ambfor optimisations can be fired from Molden
now also has a button to use cutoff's and switching.
- When writing ambfor files the order is now such that ambfor can
work with contigous molecules. The ambfor file now contains an extra
sections '[RESIDUES]' which contains the begin of amino acids and
hetatm ligands (including water).
- The ambfor and ambmd now catch the user's Control-C and now flush the buffer
before exiting.
- Ambfor now handles better finding equivalent parameters for covalently linked
ligands to aminos acids.
- Ambfor can now be run using cutoff's and switching functions: use the -N
commandline flag to use cutoffs and switching. This can be faster than
all atom optimisation ( a lot).
Fri Nov 20
- When using Gaussian with the keyword NMR, the nuclear shieldings
are read and can now be displayed as a label. If also J-couplings are
available and extra "J" button will appear in the "calculate" section.
When clicking it, select two atoms and the their J-coupling is displayed
in the calculate window.
Sun Nov 15
- Removed a bug that affected the prediction of HID/HIE histidine
residues.
Tue Nov 10
- Optimisation of Hydrogen positions under "H" icon, now also includes
getting the formal charges of HETATM residues, adds hydrogens if not added
already and calculates the partial charges of the hetatm residue.
It then optimises the OH positions of THR, TYR, SER resiudes.
Then it optimises the the choic between HIE and HID histidine residues.
Finally it adds hydrogens to the water molecules , that are in close contact
with the protein.
- the atom attributes window now also offers an editable field for the atom
number. Which makes it easier to identify an atom on screen, when only
its atomnumber is known.
Wed Nov 4
- The generation of charges on a pdb file is now more verbose. It also
does nolonger consider the amino acids, since they have charges from
the ambfor forcefield. For each HETATM residue, the charges are
calculated separately.
- Molden now also writes HETATM residue names, when writing a PDB file
via the "write" button.
- When charges are calculated for a HETATM residue, the VDW surface
colored by electrostatic potential is now supported.
Tue Nov 3
- The Hydrogens added to HETATM residues, are now put directly after
the the residue. This way it does not interfere with other fucntionality
such as interactive docking and interactive optimalisation.
Sun Nov 1
- Removed bug parsing PDB entries like 1eat, which have more than
two alternative residues
- Made routines to add hydrogens to HETATM residues crash proove
when no residue is recognized.
Thu Oct 29
- added routines to add hydrogens to HETATM residues from the PDB.
The default uses the web server from PDBeChem.
It uses the external program 'wget' for this.
If you dont have it, you can retrieve it from:
http://ftp.gnu.org/gnu/wget/
A second fallback method adds hydrogens by looking at the angles of the
atom it coonects to. This method is far from ideal or unambiguous
- added the possibility to retrieve a PDB file from the internet. It uses the
external program 'wget' to do this (see above).
You will find a "Get PDB" button and text entry field in the file selector.
- When element information is available from columns 77,78 in the HETATM
record of the PDB file, this is now used to determine the element type.
The old method, which uses the atom label to determine the element type,
is still used for old style pdb files.
Wed Oct 21
- Sometime back the MS-DOS fileformat check was introduced, for files
supplied at the commandline (for files via the file select window
this was already in place).
However, when a non-existent file was specified, an empty file with
that name was mistakenly created. This is now fixed.
- In case that there are intensities together with frequencies, both are
now listed together in the frequency list box.
Tue Oct 20
- when reading a pdb structure from the commandline, followed by
2nd mouse button click on and hetatm residue -> "Mol. -> Structure"
molden would crash. Fixed it.
Mon Oct 19
- Added optimisation of water to the H optimise option.
Waters acting as donors/acceptors to a residue, have hydrogens added.
Other waters are deleted.
- An error in reading AMBFOR .xyz files no longer leads to an exit from
the program.
- when reading an AMBFOR .xyz file, the error printing has now improved.
- removed a bug in ambfor (which can reveal it self after new memory
allocation.
Mon Oct 12
- Changed the default for a histidine residue to be Neutral (HID).
The option under the H icon, "Opt. Ser/Thr/Tyr/His H", will now
also select which histidine is the best HID or HIE (both neutral).
positive HIS has to be created via the z-matrix by adding a H to
the neutral histidine.
- In Opengl mode structures would not be updated after zmatrix editing
of a protein, fixed.
Fri Oct 9
- removed bug that would switch hetatms to visible when in backbone mode,
after setting a distance monitor.
- when switching from stick to solid in gmolden (opengl) already set
distance monitors would no longer be visible. Fixed it.
- Fixed a bug that sometimes would ambfor crash when allocating more
memory
- added the option the optimise the hydroxyl hydrogens positions of the
threonine, serine and tyrosine residues. Under the H icon.
Mon Oct 5
- removed bug which under certain conditions would not correctly show
the opengl secondary structure of the second structure read in (gmolden).
Fri Oct 2
- Some more fullgl opengl version of gmolden updates.
- removed opengl helices/strands/coils during an optimisation, since
they were not updated.
Thu Oct 1
- The fullgl opengl version of gmolden (as opposed to the mixed xwindows/opengl
version) has a few bugs fixed. In the lines mode, during an protein movie
the residues would not be updated. Now they are.
- The distance monitor now also works during a protein movie.
Mon Sep 28
- when creating a water filled box with ambfor/ambmd, some of the waters
at the edges could be very close to waters in neighbouring cells.
When using this box in MD this would result is waters with very high
velocities. This problem is fixed now.
Thu Sep 24
- Gaussian09 MP2 energies are now correctly read.
Fri Sep 18
- Fixed a problem introduced in molden4.8 with reading AMBFOR xyz files.
specifically recognising protein structure.
- fixed some of the things that dont work when running the full opengl
version of gmolden (-F commandline) flag. There still remain
some issues.
- The zmatrix is NO LONGER updated during a movie
- Scroll wheel now also work in interactive optimisation mode
Thu Sep 17
- more updates to swooth the interaction between molden/gmolden and
ambfor/ambmd
- You can now add a water box to both force field and md simulation.
- When ambfor xyz/arc files are read in, the element types are mapped
from the integer atom type, and nolonger from the atom label
Fri Sep 11
Molden4.8
- Molden4.8 introduces ambmd:
Added a simple isotropic MD program to the ambfor program.
The Molden interface can now fire these MD jobs via the optimise (AMBFOR)
window. You can now select 'ambmd' in addition to ambfor.
- the ambfor and ambmd programs now have a -b commandline flag, which
will add a waterbox to your structure
- ambmd produces a .arc file as the trajectory file. The reading of
this file in molden has been speeded up.
Wed Sep 2
- When adding the possibility of contraints to optimisation with
ambfor, it was overlooked that in the event that no restraints
were set, all atoms in the ambfor xyz file would be treated as fixed.
This has now been corrected.
- Water was not handled well in ambfor, fixed it.
Thu Aug 27
- Added a simple isotropic MD program to the ambfor program.
The Molden interface can now fire these MD jobs via the optimise (AMBFOR)
window. You can now select 'ambmd' in addition to ambfor.
Thu Aug 20
- When reading G09 output, molden now correctly deals with the fact
that G09 only prints orbitals for the input geometry and nolonger
prints orbitals of the stationary point.
- Molden now also recognizes MSDOS files supplied via the commandline
and automatically converts them to unix formatted files.
Wed Aug 12
- reading back in ambfor generated xyz files, the amber atom types
have automatically charges assigned
Tue Aug 11
- further compatability fix for reading g09.
Thu Jul 23
- fixed serious bug in reading gaussian output, while creating support
for g09. Fixed !
- reading back in ambfor generated xyz files, the supported amber ions
are now correctly classified by element.
Tue Jul 21
- first support for gaussian 09
single point, simple optimise, simple force/freq jobs supported
More updates are probable to follow
Sun Jul 19
- Removed a number of bugs concerning reading the latest Gamess-UK
output.
Fri Jul 17
- Reading gamess-uk output with more than 99 points in the
geometry optimisation, all point above 99 would not be updated, fixed it.
- The energies from the latest Gamess-UK output are picked by molden
and shown in the geom. conv. window.
- The fullgl version of molden would not update the background color when
changed with the paleete icon: fixed
Wed Jul 15
- fixed recently introduced bug, reading 3dgridfile
Mon Jul 13
- Partial optimisation can now run in BFGS optimisation mode in ambfor
upto 330 flexible atoms.
- Molden reads back in ambfor .xyz files better.
- Updating labels no longer lags in slow connection opengl mode.
- Resizing main screen in opengl is now one update.
Tue Jul 7
- Added the possibility of partial optimisation. If you want to optimise
a docked pose, select only the ligand and the surrounding residues
flexible. And optimise with the the amber/gaff force field.
- Molden now supports the scroll wheel to zoom in and out.
- When using starnet X-Win32 X-windows server, gmolden switches
to use full OpenGL (not mixed xwindows/opengl mode).
The newer versions of X-Win32 ver 8, have problems with
zooming in via the Ctrl key, in this case use the right Control key
or the scroll wheel.
- Molden can not determine which version of X-Win32 server is active.
You can use the molden commandline flag -Q, to return to the mixed
OpenGL/Xwindows mode. This will work better with older versions of
X-Win32 (6.1 and older).
- When aligning two small molecules and using the align and combine
option, there was an extra copy of one of the molecules. Fixed it.
Wed Jun 3
- Removed bug from the handling of the multi mol2 and sdf files
Fri May 28
- Added the option to compile a complete GL version of gmolden.
Uptill now gmolden did some graphics in xwindows and most graphics
in OpenGL. In the MacOSX version of gmolden, the xwindows graphics
were not visible. I therefore created the option to let gmolden
do all graphics with OpenGL calls. You request this new functionality
by adding the -F command line flag.
Mon May 4
- fixed annoyance that during animations, the animation would stop because
of the help window popup on the button started the animation.
Tue Apr 28
- fixed bug that could screw up the displaying of secundary structure
in the opengl version of molden, in the case of multiple proteins
being loaded.
Mon Apr 27
- Multi molecule files, such a .sdf files and .mol2 files will now
open an extra window in which each separate molecule is clickable.
- In addition you can now combine .mol2 files conataining poses for
a ligand with the protein being docked into:
First load protein. Second, read multi mol2 file with "Add" selected
in the read file window.
Wed Apr 16
- added the calculation of topological polar surface area (PSA).
Molden control window -> surface icon -> totpol. PSA
- added the calculation of the Quantum Mechanical PSA,
fisrt calculate a 3dgridfile with the density, second calculate
3dgridfile with QM electrostatic potential (slow),
Start up molden, go to the density mode, read in density gridfile
map esp on density, Vr icon. -> mapped
- fixed bug, after animating normal modes going into the zmatrix
editor, clicking one of the variables would move the structure
allow a normal mode.
- added the reading of multi molecular sdf files.
click the 'M' button to select other structures in the sdf file
- fixed a bug that would mess up windows on centos, when keeping
the pointer over a button and make the help text appear.
Thu Mar 5
- fixed bug causes the atoms not to be connected in the density mode
in combination with gamess-us and qchem outputs
- fixed a bug that would shown an empty structure for orca outout.
- surface off would sometimes also switch off some parts of the coil
in opengl mode; fixed it
Wed Feb 25
- MAYOR: BUG FIX FOR AMBFOR the standalone amber/gaff force field
optimizer which is called by molden.
The bug caused some torsion force constants to be to big and
could lead to distorted optimised geometries.
eg anything with a -so4- group.
- fixed a bug that would let molden crash when deleting all active structures
from the structures window, when the atom attributes window was displayed.
- some programs out there write pdb files with lowercase element and residue
labels. Molden can now handle these.
- fixed a bug that caused read in ambfor .xyz files, to be treated as
if they had no charges
Thu Jan 15
- added 64 bits executables for linux on our anonymous ftp directory
ftp://ftp.cmbi.umcn.nl/pub/molgraph/molden/bin/Linux/64bits
- fixed a minor bug in the 64 bits version when rendering helices
The Dec 18
- Zoom is now kept when editing a zmatrix
- Updated the makefile somewhat, let me know if you have problems with it
Tue Nov 25
- When a protein was edited via the z-matrix all waters were gone
except those with a connection to the protein. Now the waters are
restored when exiting the z-matrix editor.
- removed a a bug in an earlier undocumented implementation of the
above that would make molden crash during the animation of variables
in the z-matrix editor.
Thu Nov 20
- Added the posibility to color by chains (opengl only).
- fixed a bug that would render the molecule as opengl sticks after
a HETATM molecule of a protein was removed via the 2nd mouse click
popup window.
Wed Nov 12
- fixed a bug that could make molden freeze when a help window on a
button was activated
- fixed a bug with rendering forces and the in/de-crease scale buttons.
- fixed a small bug with reading non protein mol2 files, which would cause
problems when combining the molecule with a protein structure.
- Fixed bug which caused crystal information (biosym car,arc), to be
wrongly symmetry expanded if it was not the first structure be read in
- fixed a bug that would let molden crash when clicking H-BONDS in the
stick mode
- fixed a bug that would let molden hang on reading a VASP CONTCAR file
- fixed a bug that would let molden crash when as a first file a freq
jobs was read in, and consequently the spectrum was displayed.
(introduced very recently).
Mon Nov 10
- Fixed bug in memory allocation associated with the writing of .ogl
files in the surfaces window.
When you do a combine between a small molecule and a protein, the memory
would be corrupted. fixed it.
Fri Nov 7
- Fixed bug writing "charges derived" electrostatic potential mapped
surfaces in opengl surfaces window
- Fixed minor bug in writing mopac surfaces in density mode in
opengl surfaces window
Thu Nov 6
- Fixed bug which caused filetypes with crystal information (biosym car,arc)
and multiple structures to be treated as containing just one structure.
- when only surfaces but no molecule was present in a .ogl,
the scene would not be properly displayed. In perspective mode
you would be inside the surface with no possibility to zoom in.
In the non-perspective mode nothing would be displayed.
Fixed it.
- fixed bug in new .ogl writing routine, that sometimes wrote too many
connections.
Tue Nov 4
- when choosing contacts to be displayed followed by a distance
measurement, the part of the distance window where the distance
should be displyed stayed black, fixed it.
- in pdb files with dna/rna the label OP2,OP1 where not supported,
now they are.
Fri Oct 31
- The newly introduced surfaces window also now allows to write all
surfaces to a .ogl file. You can for instance now create several
orbitals and write then to a .ogl file
- .ogl files ca now be read back in to gmolden.
Fri Oct 24
- A new window lets you manage the opengl surfaces created by molden.
In the molden control window -> color palette icon -> surfaces
You can delete surfaces, change color. Separate helices can now
be colored differently. The surfaces window is also available in
the denisty mode. It automatically pops up once the opengl icon
is clicked. Surfaces can now be activated and deactivated.
- The .ogl files when selected in the read file window used longer
trigger the launch of the external moldenogl helper program.
This behaviour still goes for the Xwindows only version of molden.
For the mixed opengl/Xwindows version of molden (gmolden), the .ogl
files are dispayed within gmolden itself
- Removed a bug that would overwrite the last read file with postscript
code, when the character 'p' was pressed in the display window of
molden.
Wed Sep 17
- The align button in the structures window now also works for small
molecules.
- When viewing gromacs trajectory the backbone view is maintained if
chosen. Also the labels of the cell are no longer displayed in this case.
- You can now create a separate structure from the pdb hetatm molecules
by clicking with the 2nd mouse button on the drawing screen.
This makes it easy to save these molecules in a separte pdb file.
- Added cyclopentane and pyrrole as fragments in the zmatrix editor.
Fri Sep 12
- Added the option to map the electrostatic potential to the solvent
accessible surface
Tue Sep 9
- Added the possibility to align proteins
Fri Aug 29
- Removed another bug that made the program crash when freeing allocated memory
Thu Aug 28 (My birthday :-)
- Removed a bug that made the program crash when freeing allocated memory
- mol2 files containing multiple structures are now also supported.
An extra button (M) in the points section of the molden control window
will appear. Clicking this button will allow you to select an other
structure in the mol2 file.
- Two structures can now be combined. Select a structure, supply a
structure number in the field next to the "Combine" button, and click
'Combine'. The structure corresponding to the number will be appended
to the active structure.
Molden 4.7 first version Aug 22 2008
- Molden4.7 can keep multiple structures in memory. Each time a new file is
read in this is a new structure. You can switch betweeen structures
in the newly added structure window. The currently selected structure
is displayed. You can also delete structures in this window. The original
one structure at a time behaviour is still available when specifying
the -O command line flag.
Molden 4.6
Tue Aug 12
- Fixed a bug when going up one directory (..) in the filemanager.
This one managed to escape my attention for a long time.
- Minor changes to scrolling
Wed Jul 6
- Added dynamic memory allocation voor mopac2007 .aux files
Wed Jul 2
- Removed a bug that lets molden crash when you add the first line
of a new structure in the z-matrix (windows,macosx)
Tue Jun 24
- The mopac2007 .aux format is now supported.
The mopac .aux format can hold geometry optimisation data, charges, dipole
and orbitals information.
The MP6 and RM1 methods have been added in the submit job interface.
- Corrected a bug in displaying the dipole moment.
Thu May 29
- Activating the picture icon will allways cause a gif image to be
written, also in OpenGL mode. The latter requires a 24 bit to 8 bit
conversion, which has now been incorporated into molden.
For those who would like the rgb picture back, let me know.
Tue Apr 29
- Removed bug in gmolden that when adding the first atom in a new
z-matrix would make the atom invisible (solid/stick mode only).
- Added the ability to cap residues
- Added support for neutral asp, glu and lys (ambfor force field)
- Improved zmatrix editing of proteins: adding H to histidine will
now be recognized as the proper HIS form.
Wed Apr 16
- Small annoyance fixes.
Switched atom selecting back to the fisrt mouse button again in the
atom properties windows.
When doing a optimisation, selected atoms now become unselected.
Thu Apr 3
- Added small help boxes describing the use of button. If you keep the pointer
over a button and dont move, after 1.5 seconds, this helpful window
will appear. NOT yet implemented for all windows !!
Gradually help for more windows will be added.
- Added possibility to close/abort query box
- When the user would try to kill the main drawing window by clicking
on the x in the border supplied by the window manager, molden would popup
a window saying you should kill molden by clicking on the skull button.
On some Xwindow servers, this popup window would be off screen. Fixed it.
Tue Mar 18
- In the window to specify the atoms and methods for Oniom, the possibility
of writing amber charges as part of the element specification for Gaussian
has been added.
Fri Mar 14
- While reading tinker/ambfor xyz files, a proline could be misclassified
as a lysine. The most visible direct effect was strange behaviour of
the spline to indicate the coil secundary structure.
Fixed.
Thu Mar 13
- Labels of Cell axes are now also visible in the opengl mode of gmolden.
- Labels of XYZ axes are now also visible in the opengl mode of gmolden.
Mon Mar 10
- Fixed bug in 'edit cell parameters'
Fri Feb 22
- Added axes, only in gmolden with solid mode. It can be called by pressing
'+' or '='. No labels of axes yet: red=x, green=y, blue=z
- Added the possibility of calculating molecular surfaces, with help of the
program 'surf':
``Linearly Scalable Computation of Smooth Molecular Surfaces",
A. Varshney, F. P. Brooks, Jr., and W. V. Wright, IEEE Computer Graphics
and Applications, September 1994 [invited submission].
You will find the option under the 'surface' icon -> Mol. surf.
This option is mainly intended for use with proteins.
Fri Jan 25
- corrected bug in reading molden format files when non integer occupation
numbers would be present.
Mon Jan 21
- Added reading/writing of CIF files
Thu Jan 10
- Added writing of Gaussian cube files (reading was already present).
This can also be used to store data on a 3D grid which are slow to
calculate.
Mon Dec 17
- fixed a bug which could make the automatic z-matrix conversion crash
for very small molecules with few connected atoms
Wed Dec 12
- Fixed working with nptsx,nptsy,nptsz, edy,edy,edz in combination
with opengl
- Going to full screen in OpenGL mode would leave the molecule not
centered on the ceter of the screen, fixed it.
- Refined creating connections between backbone connections.
- Refined handeling of unclassified pdb symbols in the ATOM records
of a PDB file.
- Fog is now automaically disabled in the density mode.
Mon Dec 10
- Fixed atom selection by clicking on an atom with the second mouse button
while the "Atom Properties window" is open. This functionality was
destroyed when introducing the popup window for HETATM molecules on
Aug 8
Fri Dec 7
- Atomcolor is now switch on for all but protein structures after
reading a new file
- Better default setting of shade for proteins
Sat Dec 1
- Fixed Molden in such away that it is more compatible with the free
Xming Xserver for windows.
- Fixed a bug that would let the structure rotate after an buttonpress
in the main screen and clicking on of the amino acid options.
Fri Nov 23
- fixed bug with displaying G-functions
Wed Nov 14
- Added optimisations for displaying the opengl stick & balls for all atoms
- added support for gaussian counterpoise optimisations.
- added a commandlineflag -S to let molden start with shade off.
Fri Nov 9
- Added support for gaussian mp2 optimisations
Previously the HF energy would be listed in the geometry convergence
window, now the MP2 energy will be displayed.
- Added support for gaussian IRC outputs, previously all points were displayed
in the geometry convergence windows, now only the optimised geometries
along each point of the reaction coordinate.
Wed Nov 7
- added a window that lets you specify the total charge when using
the EEM charges.
- added two new parameter sets to calculate EEM charges with, PESP and
ESFF force field parameters
- Changed the default for automatically calculating charges for forcefield
optimisation with ambfor to PESP. This is because the previous default
only had parameters for HCNOF. In addition a string will be printed
when no parameters for an element are available.
You can always assign charges interactively and switch off automatic
charge assigning in the AMBFOR optimise window.
- Improved GAFF forcefield typing a bit.
- Removed a bug that would occasionally make molden crash when doing a
interactive GAFF/Ambfor optimisation and charge labels were also printed
(Recursive IO bug).
- when the number of atoms exceeded 10000 the writing of tinker xyz files
would not print connectivity correctly, fixed it.
Tue Oct 30
- added option to interactively change the parameters that determine
when molden draws a hydrogen bond. You will find a new entry 'H-bond
parameters' under the H icon, the 8th icon from the top from the
middle column in the molden control window.
Tue Oct 23
- fixed a bug where the reading of Gaussian files would go wrong if
the following line was present:
RelInt: Using uncontracted basis, .... etc.
Wed Oct 17
- added a 'prev' button in addition to the existing 'first', 'next' and
'movie' buttons.
- added to molden makefile, the feature to build molden, gmolden and
ambfor/ambfor when you type 'make'
- added option to convert gaussian log files to zmatrices:
gmolden molin
contents of file molin:
title
file=gaussian.log wrzmat=2
The zmatrix will be written in the file called 'zmat.out'
- added possibility to scan a part of a proteins rotamer space
(max. 6 residues). The best 10 rotamer combinations will be remembered.
The initial scoring is done via the dfire pmf score. The output can
be saved and (re)loaded via the file 'resrot'. The rotamer combinations
can be rescored with the amber force field.
To activate the window click on a residue with the second mouse button
and select the last option in the menu (add flexible residue).
Subsequently do the same for all the residues you want to be flexible.
However you first have to create a zmatrix for the protein fisrt by clicking
the zmatrix button, otherwise the new option will not be presented.
Thu Sep 13
- Fixed bug when applying edited cellparameters
- Added option to calculate charges for hetatm molecules from the PDB
(in the popup menu, activated with second mouse button click)
Fri Sep 7
Fix bug ambfor memory allocation
Mon Sep 3
Fixed bug that caused the zmatrix-ordering of atoms to be applied
without also changing the charges ordering accordingly, when
starting an ambfor (amber/gaff) optimisation.
Thu Aug 30
Fixed bug when writing zmatrices bigger than 100 atoms.
Wed Aug 29
- improved GAFF typing
Thu Aug 23
- fixed a bug that would not display a residue when replaced (in opengl)
- fixed a bug that could occur when memory is allocated for proteins
larger than 20000 atoms.
Fri Aug 17
- fixed bug that displayed "(null)" string when the cursor was above
an atom when displaying a non pdb file
Tue Aug 14
- fixed a bug that caused molden not to make a correct z-matrix for
a pdb file containing nucleotides
Wed Aug 8
- added support with ORCA through reading of the ORCA output, currently
supported are:
single point, geometry optimisation and force/frequency jobs
No support for reading electron density and orbitals
- Added support for hetatm moelcules from the pdb file, which label
will now light up when the pointer is over the hetatm molecule.
Clicking the middle mouse button will now bring up a popup menu
with options to center on the molecule, create a surface of the
molecule and to find neighbouring aminoacids.
Mon Jun 11
- Fixed bug in displaying residue labels for pdb files containing DNA
- Added the option to have a background color with a gradient.
When clicking the 'Palette' icon the first option now is 'Background Mode'
You can choose between "solid color" (the way it was) and ' color gradient'
To implement this we changed color 13 of the 15 basic molden colors to dark
blue, which is used for the default gradient color.
Of course this affects the .moldenrc file so you had best remove it and
reset your defaults. The background mode is also saved in the .moldenrc
file.
- Added the reading of electron density maps in the O format (also known as
DSN6 format) these are available form the electron density server in Upsala:
http://eds.bmc.uu.se/eds/
These maps are only displayed in the OpenGL mode (so gmolden).
Wed May 30
- Fixed a bug in writing .mol filee, of elements with a two letter abbreviation
only the last was written.
- added reading of DSN6 electron density maps, these can be read in from
the surface icon -> last option and can be displayed on top of a pdb
structure
- added information how to compile under gfortran/gcc4.0 and higher to
the makefile and molden.f file (uncomment external gfortran_iarc)
Fri May 4
- Fixed bug of displaying the dipole moment, the dipole moment
was only correctly displayed for single point QM calculations, not
QM optimisations. Fixed it.
Tue Mar 20
- Removed a bug affecting the processing of biosym .car files.
Bug was introduced when adding dynamic memory allocation for protein
coordinates
- Removed a bug affecting reading of xyz files being added to an existing
structure.
Bug was introduced when adding dynamic memory allocation for protein
coordinates
Mon Mar 12
- Removed a bug affecting the visualisation of vibrations of gamess-us
and Qchem introduced when adding dynamic memory allocation for protein
coordinates
Fri Mar 9
- Removed a bug in the processing of gaussian outputs, the bug is
'fixed' but be aware that it is not exhaustively tested as of yet
- made a minor bug fix to the reading of QChem output
Fri Mar 2
- Performance update: OpenGL density mode now makes less unnecessary
screen updates. Only important for working with remote displays.
Tue Feb 20
- Created dynamic memory allocation for proteins (all formats that support
protein information, pdb, mol2, tinker xyz, .gro)
- Display of dipole moment, if QM electron density is available, the QM dipole
moment is first calculated, if charges are available (but no QM electron
density), the dipole moment is calculated from the charges.
- Added possibility to rotate ligand within an active site:
The align icon (middle column, 9th from the top) Interactive docking ->
Pick molecule from screen -> pick a molecule from the HETATM records of
the Pdb file.
------------------------------------------------------------------------
Molden 4.5
Fri Dec 2
- Optimised protein display in the opengl version:
- residues now have their own gllist, when you display a whole
protien as solid you will see the protein being build up residue
per residue. Solid protein display will also display somewhat faster.
- when clicking the backbone button you will immediately see the
secondary structure elements
- animation of variables in the zmatrix editor in solid mode will
be a lot faster, also replacing rotamers.
- you can now choose between the richardson and dunbrack rotamer
libraries
Tue Oct 17
- Did some improvements to the QChem interface
Thu Sep 7
- Did some optimisation of orbitals and regular density space filling
plots.
Thu Aug 31
- changed the fortran code so that use of the -O2 compiler flag on linux
nolonger causes incorrect display of the surface in xwindows lines mode
(the surface looked incomplete)
Thu Aug 17
- The opengl version of molden (gmolden) would show dark blue lines
in the density-3dgrid mode with certain xwindow emulators. Fixed it
so that the lines are white again i
Wed Jul 12
- added a button "to Xmgr" which when clicked will right a file with
pairs of frequency,intensity on each lines. These files can be imported
into xmgr or xmgrace
Mon Jul 10
- when displaying vasp POSCAR or CONTCAR files, and there is a XDATCAR
file present molden will ask to use the XDATCAR, the multiple structures
can be called with the 'fisrt','next' and 'movie' buttons.
- when doing interactive docking sometimes extra hydrogens were added
to the second molecule with erroneous connections to the first molecule,
fixed it.
- when doing interactive docking you are now asked if you want to align
the centers of both molecules or not (yes used to be the default)
- the make option 'make noxwin' now should work again. This can be used
to create a version of molden without xwindows and opengl, you can
only control this version with a keyword file.
Wed Jun 28
- The internal opengl representation of mopac .gpt files had errors
in representing the connections of the molecule.
- Tinker xyz files which use the amber or charm forcefields are now
correctly visualized when atoms like F, P Cl and Br are used.
Tue Jun 6
- B. van Eijck added the keyword CHADD, which will read extra charge
centers from a 'molden.def' file.
Tue May 30
- Removed some small bugs, reported by Robert Gyepes
- added a special makefile for cygwin makefile.cygwin
Fri May 19
- Added 'best rotamer' option, this calulates for a particular residue,
the best scoring rotamer according to the dfire protein-protein score.
- Removed a bug which on some platforms would make molden crash when
writing out a z-matrix
- Some rudumentary support for gfortran (you still have to edit molden.f
and comment out the line 'external iargc' )
Wed Mar 8
Spherical G-functions (9G) in combination with electrostatic potential
and mulliken charges are now also fully supported
Mon Mar 6
- Support for Gaussian cartesian G-functions (previously i was unaware of
G-functions in the Gaussian series of packages).
- Support for the Gaussian03 revision D, the output format of the basisset
has slightly changed. Adpated molden to deal with it.
Tue Feb 7
- First support for QChem outputs: For molden to be able to read orbital
and basis-set information, supply the following qchem keywords in the $rem
section:
PRINT_ORBITALS TRUE
PRINT_GENERAL_BASIS TRUE
You can supply output of composite qchem jobs, molden detects it and will
allow you to select the different job outputs by clicking on the 'M' button
which appears in the "Select Point:" section in the molden control window.
NOTE: support is still rudimentary, i dont have qchem, only a few outputs
sent to me by a user. If you think this functionality is important
than let me know when it doesnt work
Thu Jan 19
- Support for dynamic memory allocation for the part that shows geometry
convergence, implemented for use with gromacs and cpmd.
- In popop menus you always had to choose a selection (sometimes cancel)
Now you can click besides the popup window to get out of the popup and
cancel the selection. Therefor the option "Cancel" there where used to
be offered has been removed.
Tue Dec 20
- Support for the latest Gamess-US version (tested 27 JUN 2005 (R3) version).
The basis-set print out of Gamess-US version had changed.
Fri Dec 16
- When writing PDB files, in case of no chain information read in
molden will now generate and write chain labels
- With gromacs files the generation of connectivity is now much quicker
also solvent molecules will be rendered in less detail in opengl molden
which will speed things up a little
Fri Dec 9
- Molden can now read the binary gromacs files .trr and .edr. Previously
molden would first convert them to their ascii counterparts with the gmxdump
utility. This way the very large ascii files are nolonger needed.
Tue Nov 29
- Added molden keyword 'MOGL' which will let you create a molden.ogl
file from a molden keyword file.
Mon Nov 28
- When replacing one amino acid residue by another, followed by writing
a pdb file, the replaced residue number would be wrong: fixed
- When writing .mol2 files, sometimes a double bond to many was written
(conjugated systems), since molden does not do anything with bond types
this was not serious, but other programs (sybyl) do work with bond types.
- When Cbeta or backbone O (C=O) was missing on a pdb residue, connections
to a non existing atom at cart.coord (0,0,0) would be drawn in the opengl
version of molden (gmolden)
Mon Nov 7
- With gmolden the aminoacid currently under the pointer is shown by
temporarily showing the label, when clicking with the second mouse button
a popup window with a few options pertaining to amino acids would appear,
every now and then this window would not be visible untill you moved the
pointer over it (only on certain xservers), fixed it.
Wed Nov 2
- Fixed writing of Gaussian inputfiles for oniom calculations (from the submit
Gaussian Job windows). This bug was introduced when charges for proteins
were added (amber forcefield) in molden4.1 (Why does no one ever tell
me it does not work ???)
- Changed the working of the residue commands window:
128-130:A would mean residue 128 through 130 of chain with Label "A"
NOW all numbers refer to residue numbers used in the PDB file:
128-130:A now actually means the same as 128-130.
You still can use the chain label for things like coloring:
*:A col
Will let you pick a color with which all residues belonging to chain "A"
are colored with this color
128
residue with PDB residue number 128 will be shown.
Fri Oct 28
- fixed a bug that would override user assigned sybyl atom types, when
writing mol2 files
- added the possibility to change the potential levels at which certain colors
where used for the colorcoded opengl esp potential
- The PC-UNIX version of Gamess-US misses the first column with respect
to the regular Unix version, made some adaptation to let molden work
with this output to.
- Fixed geom conv for a series of xyz structures where so of them had 'heat'
0.0
Fri Sep 30
- reorder Z-matrix, clicking a few atoms and then hitting
escape, this would create a zmatrix in the order of clicked atoms
and the rest would be figured out by molden. This did not always
work. I fixed it in such a way that it can handle nearly all cases
but there are still some conditions not supported, but this is not
so relevant since you can always do it again.
- When doing interactive docking, you can now change the center around
which the ligand rotates (in the same way as the overall rotation center).
And you can now reorder the z-matrix of the docked ligand.
Wed Sep 23
- Added the possiblity to do a surface per residue in the surface window
(opengl version only), takes longer but also looks a lot better.
- When aligning or docking and then writing as a PDB file some of the atoms
were missing, corrected it.
- When docking a molecule, the to be docked molecule is placed at the center
of the molecule docked to.
Wed Sep 21
- Fixed running tinker in the background for the opengl version of molden
- Made residue commands concerning surface also work for the opengl version
- Added Fit Rotamer option, which will replace the amino acid conformation
with the closest rotamer in the rotamer library
Mon Sep 5
- Added support for the tinker amoebapro force field
- reading in tinker xyz amber files would be retyped to charmm types
fixed this
Mon Aug 15
- Fixed xwin.c for molden without OpenGL
- Fixed writing of GIF files for using Xservers with 16 bit planes
Fri Jul 15
- Added interactive opengl support for the density mode (only available
with 'make gmolden').
- Fixed bug which can lead to not displaying gaussian outputs correctly
in some cases.
- Fixed a number of small annoyances (dont worry, there are enough left).
Wed Jun 15
- fixed bug that let f-functions run in to the code meant for the g-functions
resulting in reporting number of orbitals is wrong
- fixed reading MOL files, this bug was introduced with support for reading
gromacs files
Thu Jun 2
Addition of creating opengl surfaces in the molecular mode, when clicked
add to the backbone (protein structure only), and clicking with the second
mouse button on a backbone atom a drop menu will appear, which let you
do things like (un)display the residue, center it, and add to the surface
(of course only available when molden is compiled with opengl support (gmolden))
------------------------------------------------------------------------
Molden4.4
Mon May 9
The main reasons for this new minor version of molden are:
- Introduction of the incorporation of interactive Opengl in the main
interface of molden (molden already had opengl helper program moldenogl)
You can build the gmolden version by typing;
make gmolden
This version is still under development
- Reading of NLMO's of the NBO analysis in gaussian
- Partial support for G-functions. As far as orbitals and electron density
G-functions are supported. Also mulliken charges, except when using 9G
functions. The electrostatic potential is not yet supported.
Addition of a new keyword to the molden format: [9G]
which specifies the use of spherical G-functions instead of gaussians.
The order in which molden expects MO coefficients to pe printed is:
For spherical G-functions:
G 0,G+1,G-1,G+2,G-2,G+3,G-3,G+4,G-4
For cartesian G-functions:
xxxx yyyy zzzz xxxy xxxz yyyx yyyz zzzx zzzy
xxyy xxzz yyzz xxyz yyxz zzxy
The request for support for G-function came from the molcas development
people, but also Gamess-US will benefit from this support.
------------------------------------------------------------------------
Molden4.3
Fri Apr 29
- introduced number of small bug fixes:
the environment g03root was not recognised and g98 was written in the
.run files created by molden
- premature end of file in gaussian can let molden crash, removed one
instance on which it could crash
- Introduction of the incorporation of interactive Opengl in the main
interface of molden (molden already had opengl helper program moldenogl)
You can build the gmolden version by typing;
make gmolden
This version is still under development
- Reading of NLMO's of the NBO analysis in gaussian
- addition of dynamic aminoacid labels and clicking on a backbone
atom will bring up a small dropdown menu with visualisation options
Wed Feb 23
- Fixed bug that effectively disabled the aligning of two molecules
- Fixed a bug in the z-matrix editor that would not correctly show all
atoms in the when the 'stickcolor' mode was disabled.
Fri Jan 28 2005
- Lots of small bugfixes, as there are:
Fixed editing z-matrix of ligand when doing interactive docking,
Not edit operations where bug free
Fixed updating of properties when editing the z-matrix
- Added support for the Gromacs (gmx) file format .gro:
Molden will read the file name.gro and will then look for the file
name.top to read connectivity, charges and atom types. When not found
Molden will create connectivity.
Next molden will look for a trajectory file name.ttr. If found it will
use gmxdump to convert it to an ascii trajectory file name.trra.
Molden will not do the conversion if a ascii trajectory file name.trra
already exists.
Next molden will look for an energy file name.edr. If found it will
use gmxdump to convert it to an ascii energy file name.trra.
Molden will not do the conversion if a ascii trajectory file name.trra
already exists.
If a trajectory file is found, then molden can animate the MD run by
clicking on the movie button.
- Hitting the escape key when running an animation will exit the animation.
Hitting the space key will stop the animation and when hit again will resume
the animation.
Fri Jan 14 2005
- Some more work on the writing of mol2 file for proteins.
- Incomplete amino acids are now reported.
- changed xwin.c so it does better on 64 bits AMD/Opteron systems.
Tue Dec 21 2004
Introduction of Molden4.3:
- The reading of Gaussian output files has been restructured, it is
possible that this may temporarily be a step back in molden reliablity.
PLEASE inform us of any problems related to reading gaussian outputs.
- Did some work on writing better mol2 files for proteins, there are
still problems, but at least molden can now read it back and create
a z-matrix for the protein without crashing.
Sybyl still has problems with these files ! It needs more work.
- Added forces information to the molden format, example:
[FORCES]
point 1
3
-0.000038 -0.000160 0.000430
0.000834 0.000150 0.000047
-0.000263 0.000008 -0.000017
point 2
3
-0.000505 0.000339 0.000987
0.001268 -0.000634 -0.000242
0.000123 -0.000017 -0.000640
....
point 10
3
-0.001299 0.000970 0.001904
0.002139 -0.001328 -0.001049
0.000512 0.000004 -0.001636
The number of points must match the number of points used in the [GEOMETRIES]
section.
Second form includes coordinates, this is only needed when the forces are
not in the same orientation as the geometries supplied in the [GEOMETRIES]
section. For instance, the Gamess-US forces are not in the z-matrix orientation
, so when [GEOMETRIES] ZMAT is used the forces would not be in the correct
orientation.
[FORCES] COORD
point 1
3
-0.000038 -0.000160 0.000430 0.0 0.0 0.0
0.000834 0.000150 0.000047 0.0 0.0 1.0
-0.000263 0.000008 -0.000017 0.0 0.0 -1.0
....
NOTE: this extension is on trial, it may not be the final solution.
Developers who write their own molden format should not be
overanxious to implement it.
- fixed problems with reading circulair peptides.
- increased the max number of geometries and scf iterations molden can handle
to 2000 and 1000 respectively.
------------------------------------------------------------------------
Molden4.2
Tue Oct 05 2004
- Corrected a few fortran syntax errors, thnx to Gyepes R.
- on some platforms molden would not write a z-matrix, after stating
that it just did. fixed
Thu Aug 05 2004
Molden 4.2 introduces quite some radical changes in the way proteins
can be manipulated with the z-matrix editor. Where in previous versions
any change to the z-matrix was followed by a complete update of the
cartesian structure, with molden4.1 only those parts of the cartesian
structure are updated that have actually changed.
The advantages are that protein manipulation is much faster and now
larger proteins can be manipulated, these manipulations include,
deletion, insertion and replacement of amino acids. Also the animation
of variables such as the chi sidechain rotamer angles can now be done
interactively. A new feature is the possiblity to change side-chain rotamers.
The procedure is now:
1) load in a PDB file
2) click the zmatrix button and create a zmatrix for this protein
3) click the backbone button
4) NEW click on the backbone with the SECOND mouse button and a popup
window with side-chain commands will appear:
B
switch on display of this amino-acid, replace amino acid, replace rotamer
5) Switch to full zmatrix to edit individual atoms
6) click in the zmatrix on the Chi1-4 edit boxes with the second mouse
button and select "animate", click the edit box again to end the animation.
7) click in the Molden Control window the button "Hetatm" and switch on
Helix, Beta sheet, and coil and optionally any hetatm records.
8) click on the Vr icon (7th from the top) and select OpenGL
(you need to have the molden opengl helper program installed for this,
moldenogl) to get a high quality opengl display of your protein.
The z-matrix is only used for manipulation of the protein, a zmtrix of a
protein should never be saved, instead the updated result should be stored in
PDB file.
The disadvantage of this new approach is a much more complicated algorithm,
in which undoubtable some bugs have found there way home.
------------------------------------------------------------------------
Molden4.1
Wed Jul 21
- The zmatrix conversion for proteins containing nucleotides
has been improved, it will now create a zmatrix.
Still No manipulation of nucleotides however.
- The windows version of molden now start the opengl
helper program mogl, when you click a *.ogl file
in the read file window.
Thu Jul 15
- Now when you apply the tinker amber force, automatically
the charges associated with the atoms belonging to
amino acid residues are set.
- A user reported that within gaussian03 you can have the
condition that you use pure D functions (5D), but
use cartesian F functions (10F). Molden did not handle
this correctly, it would assume the use of all pure
functions (5D and 7F) or all cartesian (6D and 10F).
Molden can now handle this mixed use of pure and cartesian
D and F functions.
This also has ramifications for the molden file format:
Previously the default was 6D en 10F, the use of the keyword
[5D] would mean 5D en 7F. The new format uses:
- default is 6D and 10F
- [5D7F] means 5D and 7F
- [5D10F] means 5D and 10F
- [7F] means 6D and 7F
for backwards compatibility, [5D] still means 5D and 7F.
- Fixed a bug that would molden not read the Pseudo
Potential information of a G03 run (older versions
were ok).
- Added the [PSEUDO] section to the molden format:
[PSEUDO]
Fe 1 16
....
This is elementname followed by the number of the atom
and the effective core charge.
Wed Jun 16
- fixed bug that would let the windows version of molden
crash when you go to the density mode without having
read in a file (for the benefit of reading gaussian
cube files)
- Molden now checks whether the contraction coefficient
it reads in via gaussian output files and molden format
files contain the normalisation of the contracted
gaussian.
- increased the maximum number of atoms in the density
mode from 300 to 2000, this to the benefit of oniom
calculations. (this is independend of the max number of
basis functions in molden).
Wed Jun 9
- Added interactive docking:
- start molden with a PDB/mol2 file containing the pocket
- Click the icon with the two phenyl rings overlayed:
(In the Molden Control window, the nineth icon from the
top). Choose 'Interactive docking'
- Supply the name of the PDB file containing the ligand.
- Follow on screen instructions for rotation/translation
- the Docking Score window will appear, when you rotate/
translate the ligand, the PMF score will be updated
in this window.
- the window also allows you to store and write combinations
of rotation/translation of the ligand (pose).
The filename pose.xx will be used for written poses.
- The AtomInf button lets you display info on the PMF score
contributions of a picked ligand atom: click on one of
the ligand atoms. The PMF score window will pop-up with
a list of the top negative (=favorable) and top positive
atom-pair contribution for the slected ligand atom.
When clicking on a list entry the corresponding protein
atom of the ligand atom - protein atom pair lights of
on the screen (clicking again will switch it off).
- activating the 'ligand color mode', will color ligand
atoms according to the amount the contribute to the total
PMF score for the ligand.
Thu Mar 25
- In the z-matrix editor, you can now use the second mouse
button to select in molecule drawing screen an atom.
Now a change fragment popup box will appear to facilitate
structure manipulation.
- added the ability to read the high level layer orbitals/
basis-set of an oniom calculation. Apparently the orbitals
are only printed at the first point, NOT at the stationary
point of an optimise run.
- improved the interface to run amber within gaussian.
Parameters are automatically assigned (for amino acid atoms!)
- When using ONIOM with High and Low layers, the charge &
multiplicity check went wrong, fixed it.
PLEASE LET ME KNOW if you use the oniom interface in molden
and have suggestions for inprovement.
------------------------------------------------------------------------
Molden4.0
Wed Mar 17
- When there is an error reading the vectors (orbitals)
in gaussian, molden would automatically skip the reading
of ESP charges from gaussian. Fixed this.
- The print format for ESP charges has changed going from
g98 to g03. The new format is now supported.
`
Mon Mar 15
Fixed a bug that lets molden think that any file that
begins with an empty line is a mopac .gpt file.
Mon Mar 1
- Molden didnt correctly parse Gaussian oniom output:
corrected it.
- Added better support for the MacOS system, by adding
an entry to the makefile for the moldenogl program
and adding #ifdef statements to the corresponding
C code, ogmol.c and silly.c
Tue Feb 17
- Fixed the reading of gaussian outputfiles when using
the amber forcefield.
Fri Feb 13
- Fixed small bug that wouldnt let you display beta
orbitals with the molden commandfile.
Thu Feb 5
- Changed common block /freq/ in such a way that
compilers no longer complain
Mon Jan 19
- Fixed a problem with the new Multi molden_format,
In case of multiple molecules with vibrational
information, this information was not updated.
- The name of the file read via the filemananger
will now be displayed as the name of the main
graphics window. Same holds for named [MOLECULE]
sections of a multi molden_format file.
- Changed the code of wrzmat.f, this gave problems
on some platforms (AIX).
Wed Jan 14
- Fixed a bug that presented it self with g98,g03
xyz optimisation of a molecule with more than 50
atoms. When clicking in the geometry optisation window
on a point, the shown geometry would be out of sync
with the next/movie button geometries.
Mon Jan 12
- Fixed a bug that made molden crash every once in
a while on LINUX !!!
- Reduced the flickering of windows when
an other window is moved over it for LINUX.
Thu Jan 08
- support for gaussian with pseudopotentials:
Now the proper mulliken charges and density are calculated
- In rare cases gaussian reduces the number of MO's,
making it smaller than the number of basis functions.
Molden can now handle this.
Wed Jan 07 - fixed bug reading Molden Format files:
when reading two Molden Format files after each other
and the number of occupied orbitals in the first was
bigger, the second file would have the wrong density
matrix due to some old occupation numbers being present.
- Molden allocates memory for the orbitals dynamically
but not so for the basis-set. This could lead to problems
with very large calculations. I increased the storage
for the basis-set with a factor of 4.
- Added new feature to the Molden format:
Molden format files can now be concatenated in to
one file, provided they are separated by the
[MOLECULE] keyword line. In addition each molecule
can have a [TITLE] line, example:
[MOLDEN FORMAT]
[MOLECULE]
[TITLE]
title molecule 1
.... rest as usual
[MOLECULE]
[TITLE]
title molecule 2
.... rest as usual
If Molden reads such a file, a extra button will appear in
the "select point" section of the molden control window.
When pressed, the titles of the molecule sections will
be listed and when selected the appropriate molecule
section will be read.
Each [MOLECULE] section can have all the previously supported
sections/keywords.
2004
Tue Nov 25
- When reordering a Z-matrix nolonger all atoms have to be
clicked. When hitting the escape key molden will try
to figure out the ordering of the remaining atoms.
- Gaussian03 no longer prints just electronic energy
during SCF, but total energy, when using the #P keyword.
Molden wrongly subtracted the nuclear repulsion energy.
Fixed.
- Added a button near the "first, next and movie" buttons.
When clicked this button will open a window in which the
delay time (in milliseconds) between one structure and
the next. This delay time also has effect on the display
of normal vibrations.
Mon Nov 17
- Molden now fully supports 5D and 7F orbitals.
Previously, only orbitals and density were supported,
NOT mulliken charges, electrostatic potential and
multipole expansion.
Fri Oct 17
- Via the button "read", there is now the option "add"
available as opposed to "replace" which stand for the
original behaviour. "ADD" adds a structure to the
existing structure on the screen.
Currently this option is ONLY supported for the following
file types: pdb, mol2, and xyz
This option is mainly useful for comparing different
conformations (protein) AND offers the ability to
read in a protein and overlay different docked ligands.
- A mayor overhaul of the PDB editing capabilty via the
Z-matrix editor. This will probably need more work, but
is quite an improvement over the existing situation.
- The Z-matrix editor will now try to keep the original
orientation and translation when translating zmat to
cartesians.
- Molden picks up the normal modes symmetry tag for
Gaussian and Mopac output.
- prelimenary support for Tinker4.1. Tinker4.1 has
different names for the amber and charmm parameters files.
Also a few (non residue) atom types have changed, this is
NOT YET supported.
- use of the gaussian keyword hpmodes caused problems
for molden: fixed
------------------------------------------------------------------------
Molden3.9
Tue Aug 26
- calculated spectrum now also supported for mopac
Mon Aug 25
- corrected bug that didmt read old gaussian freq
outputs
Wed Aug 20
- Corrected a bug in the new calculated spectrum part.
This bug only manifested itself when the number of
frequencies exceeded 200.
Mon Jun 30
- Corrected Gaussian03 frequency reading
- Now with PDB file writing, the original residue number
is maintained
- You use an expression like *:A to turn on all residues
of the A chain
Tue Jun 17
- Added a feature to display an interactive spectrum
- Added to the Molden format an item:
[INT]
intensity1 [raman_intensity1]
intensity2 [raman_intensity2]
...
intensityn [raman_intensityn]
- Added the support for gamess-us Natural orbitals
------------------------------------------------------------------------
Molden3.8
Thu May 22
- Gaussian03 basis-set output has slightly changed
with respect to Gaussian98, this would cause error
in molden with molecules with more than 9 atoms.
Fixed it.
Wed May 21
- When forces or displacement were to large, Gaussian
would print *******
Molden couldnt deal with that, now it can.
Tue May 20
- Support for mopac2000 ASCII gpt files
Tue Apr 29
- 3Ddrc gamess-us IRC support
Wed Apr 16
- First support for Gaussian03
Tue Apr 01
- PDB residue numbering is now consistent with those
in the actucal PDB file
- MOPAC grid search output is now somewhat supported
- Drawing errors for coil secundary structure are
reduced
- In the Z-matrix for PDB entries, HETATM's will
be attached to the backbone instead of the closest atom.
Mon Feb 17
- Added the ability to write MDL mol files.
- Added the ability to calculate EEM charges,
a sort of gasteiger charges, by Patrick Bultinck
- The reading of PDB files now handles additional
Hydrogen labels
Wed Dec 04
The oniom stuff had a bug for the linux version, fixed.
Thu Nov 28
Added an update to the ONIOM window.
Tue Nov 05
- Complete update of the Gamess-UK dedicated code by
Huub v. Dam:
- Reading of SCF-convergence for CASSCF and DFT
- Reading of CASSCF orbital occupancies
- Support for HESSIAN jobs added
- and more ...
Thu Oct 17
- Added support for the CPMD program
Distributed with the permission of TEODORO LAINO
NEST Laboratories - INFM - Scuola Normale Superiore
Some work still needs to be done.
Fri Oct 11
- Added makefile entry for Mac OSX, thanks to Eric Brown.
Wed Sep 25
- Molden3.8 has support for tinker3.9, older versions of
tinker are not supported (Molden3.7 support tinker3.6)
(Thanks to Nicolas Ferre)
- Nicolas Ferre added support for ONIOM calculations with
gaussian98.
- In submit gaussian window you can specify
you want to write cartesian coordinates instead of z-matrix.
- You can now run amber from gaussian, in the following way
Read in a pdb file, click the z-matrix button and create
a z-matrix, assign tinker amber atom types (the FF button)
Go to submit job option gaussian, choose method "amber"
"Write XYZ" form the "Gaussian Job" window.
In principle this can be combined with the oniom method
but this is not tested yet.
- When introducing Mopac2000 support a bug was introduced
which interfered with the reading of tinker xyz files, fixed.
Molden3.7
Wed Sep 25
- When introducing Mopac2000 support a bug was introduced
which interfered with the reading of tinker xyz files, fixed.
Mon Jul 08
- Correction added to the postscript plot.
- added F and Cl as hydrogen-bond donors
Mon Apr 08
- Gamess-US version 16 FEB 2002, has a slightly different
basis-set section. Molden now supports this.
Fri Apr 5 - Added support for reading Mopac2000, out and arc files.
Wed Mar 20
- added some small changes to the automatic xyz->z-mat
conversion
Wed Mar 13
- when mol2 files would miss residue information
molden would display the structure, fixed
- when reading xyz files containing multiple structures
containing energy values in the title line, energy values
of zero, would not be correctly read on the second time
a multiple xyz structure was read. Fixed this.
Tue Mar 05
- The introduction of a extra line "FORCE CONST.:" when
running a force job with gamess-us, caused molden
to not find the normal coordinates. Fixed this.
- When running a Gaussian job using F functions, molden
incorrectly calculated the ESP charges. Fixed this.
- added an option to read the ESP charges calculated by Gaussian
Under the surface icon there is a new option "read ESP charges"
YEAR 2002
Thu Nov 15
Adapted the script multi_vrml_orbitals.csh to deal with
the changed VRML orbitals.
Tue Oct 02
The Gamess-UK orbital occupancy section has changed,
molden now deals with it.
Thu Aug 30
- Assigning sybyl force field atom types sometimes failed
to assign aromatic types, fixed it
- Now support for different spacegroup setting in mol2
file (the CRYSIN line, setting field (75-142 alternative
settings are NOT supported)).
- Molden now reads mol files, only 3D tested. The mol file
is recognized when the string V2000 or V3000 is present.
Wed Jul 25
The Gamess-UK optxyz output has changed, molden gave errors
with these new outputs, fixed it.
Tue Jul 17
- Added a conversion program to convert CADPAC output to
molden format (cad2mol). This program was written by
Mariusz Klobukowski (Mariusz.Klobukowski@ualberta.ca).
This program is now distributed together with the molden
source, to compile it type:
make cad2mol
To run it:
cad2mol 'cadpac_output'.out
A file 'cadpac_output'.mdn will be created, molden will
be able to read it.
Mon Jul 09
- Molden did not allow to subsequent subtractions of 2D grids
(gridfile) from the current (density) grid.
Rho_AB - Rho_A - Rho_B was not possible. Corrected for it.
- Molden nolonger recalculates the density before reading /
writing a 2D grid, this make it possible to write
subtracted grids.
Fri Jun 29
- Added the possibility to render orbitals transparent
in VRML2.0 by clicking on them
Commandline flag -k adds background + a light.
This is to overcome a very dark scene on some terminals.
Thu Jun 21 - added small correction to the reading of
GAMESS-US outputs (when SCFTYP= and RUNTYP=HESSIAN
were not on the same line in the input file, molden
would not display the vibrations).
Thanks to Georgy Salnikov, NMR Group,
Novosibirsk Institute of Organic Chemistry, Russia
Thu May 31 - Added support for writing mopac2000 input
containing crystal information (Tv vectors)
Tue May 15
- Added support for mopac2000 output containing crystal
information (Tv vectors)
Mon May 14
- Removed a bug in reading pdb files containing just
HETATM records.
Thu May 10
- REMOVED MAYOR BUG in reading new basis-set section
of GAMESS_US !!!!!
Thu May 9 - Molden can now launch a G98W session on windows
Thu Apr 19
- Addded new makefile section for HP-UX
Mon Apr 2
- The Z-matrix editor option "substitute atom by fragment"->
"Read" sometimes passed the wrong filename, fixed it.
Tue Mar 13
- Molden sometimes crashed on the OPTXYZ output of
Gamess-UK. Fixed thanks to Huub van Dam.
Wed Mar 07
- Molden now deals with changed writing o MCSCF orbitals
of Gamess-US.
- Gaussian98 by default only prints the Z-matrix and resultant
coordinates ONLY for 50 atoms or less. However molden
didnt respond correctly when this default was overridden
with the keyword: IOP(2/11=1). Fixed.
Tue Dec 19
-Added Option to specify opt=z-matrix in the "submit job"
for Gaussian, available from the Z-matrix editor.
This forces Gaussian to use the Z-matrix when optimising.
The default is to use a nonredundant set of
internal coordinates
- Molden should now nolonger crash on empty files
Mon Nov 27
Molden format in combination with both alpha and beta
spin orbitals gave problems when more than 128 orbitals
were present solved it.
Tue Oct 31
Added the ability to visualize protein secondary
structure elements such as helices,strands and coil
with the OpenGL helper program. The procedure is
as follows:
- you read in your protein
- you click the "BackBone" button
(If you do not, all of your protein atoms will
visible in the OpenGL, making it extremely slow,
except for small polypeptides)
- you select ligands via the "HetAtm" button
No need to select "Helix","Beta","RNA/DNA" or "coil",
they will automatically be included in the OpenGL.
- select separate residues to be displayed by clicking
"Residue" and then clicking on the backbone on the
screen.
- Decide wether you want the residues and ligands to
be displayed as tubes (default) or as spacefilling
The latter can be switched on by clicking "Solid"
-> "Space Filling"
- Decide wether you want the residues and ligands to
colored by their elements or by residue/ligand color
This is controlled by the "StickColor" button.
- Now click the "Vr" icon and select "OpenGL"
Molden will create a file called "molden.ogl"
and start up the OpenGL helper program "moldenogl"
Remember to rename this file if you want to keep
it, otherwise molden will overwrite it the next time.
- At anytime you can visualize this file again, without
having to start molden by typing:
moldenogl
or:
moldenogl molden.ogl
- use the moldenogl cammand line flag "-r" is you
want to use high quality spheres and cylinders.
This will increase the graphics quality at the expense
of speed of rotation.
- Use the left mouse button to rotate your molecule.
In combination with the "Ctrl" and "Shift" button
respectively, a zoom and translation are performed.
- The third mouse button will bring up menu with
lots of option, of which the "Screen Capture"
option allows you to save your picture as screen
dump postscript or "Vector Postscript". The latter
take longer but will yield a better picture on a
native postscript printer.
- molden has a new commandline option "-z", this
will let molden use more polygons and will
result in a better opengl picture (at the expense of
speed, but ideal for a good postscript picture
in combination with the moldenogl -r flag).
- you can edit the "molden.ogl" file,
specifically the following section is important:
[COL STRANDTOP] 0.0 0.0 1.0
[COL STRANDBOTTOM] 1.0 0.0 1.0
[COL HELIXOUT] 0.0 1.0 0.0
[COL HELIXIN] 0.6 0.6 0.6
[COL RNA] 0.5 1.0 0.5
[COL COIL] 1.0 1.0 1.0
This defines the color of the beta strand (first two),
the helix outer and inner surface (following two),
and the RNA and Coil parts respectively.
They are used further down the file:
[RIBBON] HELIXOUT
Alternatively you may supply a color per ribbon,
by supplying rgb triples (red,green,blue):
[RIBBON] COLOR 1.0 0.0 0.0
In molden you can now also select "coil".
In addition you can click on the helix,strand or
coil to activate a residue (in combination with the
"Residue" button.
Also added the writing of POVRAY files of the ribbon
cartoons as desribed above. Follow the same procedure
to generate then, except that you have to choose
"Povray" under the "Vr" icon.
Molden3.6:
Fri Sep 15
- Gamess-us (After Jan10 2000) outputs gave problems
on 64-bit Alpha-linux systems, corrected it.
G77 compiler flag -mieee has to be added.
Tue Sep 12
- Added screen capture possibilities to the OpenGL
helper program moldenogl. Three options:
- IRIS RGB format (key F10)
- greyscale encapsulated postscript (key F11)
- PPM bitmap file (key F12)
added a menu option "screen capture" holding the
above three options
Thanks to Pedro Vazquez for supplying the code for
postscript and PPM writing.
Mon Aug 21
- Problem with reading shelx files generated by
the CSD's conquest code:
SYMM .5+x, .5+y, z
Molden expected all capitals, fixed to handle
lower case. (All commands must still be in uppercase
however).
- Trying to edit the cell parameters of a structure
read in as shelx file, made the program core dump, fixed.
Thu Aug 17
- Added keywords to enable mapping of properties
onto a isosurface with Gaussian Cube files, example:
title
GAUCUB=meto_dens.cube MAPFIL=meto_esp.cube VRML2.0
SPACE=0.001 MAPVAL=(-0.3,-0.1,0.0,0.1,0.3)
GAUCUB for the Gaussian cube containing the density
MAPFIL for the Gaussian cube containing the property
(like the electrostatic potential)
MAPVAL use to change the default property values
associated with the 5 basic colors used
for interpolation
(default values: (-0.1,-0.05,0.0,0.05,0.1))
Remember currently mapping only works with VRML2.0
and OpenGL output.
- Added a program called 'short_wrl' written by
Andreas Klamt of COSMOlogic, to remove redundant
vertices from moldens VRML2.0 files
To build it type: make short_wrl
To run it: short_wrl molden.wrl
Now molden.+.wrl contains the new VRML2.0 file
Fri Aug 11
- The GAMESS-US basis-set output section has changed
molden has been updated to deal with this
- Molden now also writes a '[LINES]' section to
the molden.ogl file. This is the input file for the
molden OpenGL helper application moldenogl.
Older versions of moldenogl may have problems with
this new section.
The [LINES] section has been constructed to visualize
the cell and alpha helices and beta strands.
- Added a few options to the moldenogl, when clicking
with the third mouse button in the main drawing window
you find a menu with as new option 'Animation'
this options under it will allow you to stop/start the
animation, advance by one point (also key 'n' or 'N')
and lets you slow down animations.
Fri Jun 30
- GAMESS-US has a changed writing when using pure 5D
molden now deals with in (Thanks to Fred Arnold)
- the moldenogl helper program can now also be called
from the 'molecular mode', it will do normal vibration
animations and animations of molecular reactions.
(Via the VR icon->Opengl).
the molden.ogl format now accepts more molecules.
Added the option -l,-p,-b number to moldenolg
-l = low resolution molecule (faster)
-p = perspective mode on
-b number = choose background color
Added also to the popup menu, including a fullscreen
option, and a light2. (three lights 0,1,2)
Mon Jun 26
- The routine reading XYZ files had a problem reading
actinium 'ac', fixed it
- Added a number of things to the opengl helper program
moldenogl, accesible via the menu (third mouse button click):
+ transparency toggle (or 't')
+ switching on/off of lights 1 through 3 (or '1','2','3')
+ fullscreen option (or 'f')
+ perspective mode (or 'p')
Thu Jun 15
- Added the possibility to create an isodensity surface
colorcoded with the electrostatic potential.
Needed are two gaussian cube files or two molden
3dgridfile's (you can create these by clicking
'write grid' after a 'space' calculation.
Molden will always create a file called '3dgridfile')
Currently only "Opengl" and VRML2.0 output is supported
You will need the updated version of 'moldenogl'
to view the OpenGL output.
For an explanation how to to this see URL:
http://www.cmbi.kun.nl/~schaft/molden/mapped.html
For an example VRML2.0 file:
http://www.cmbi.kun.nl/~schaft/molden/wrl/gamuk.wrl
Added to 'moldenogl' opengl helper is a menuitem
(Third mouse button click) 'transparency'
In the molden file select window, a click on a file
ending with the name '.ogl' will bring up moldenogl
with this file.
Fri Jun 09
- When a job required more than the default 256
orbitals, molden allocated more memory, but as a result
the HOMO and LUMO buttons of the xwindows interface
nolonger worked correctly. Fixed it.
Mon Jun 5
- Jeffrey Frey and James Hess have suggested a small
adjustment of the [MOLDENOGL] format.
You can now adjust the transparency of a surface by adding
a number:
[SURF] TRANS 0.75
Wed May 31
- When reading molden format files with more than 256
orbitals, some arrays were overwritten, fixed it.
- In z-matrix editor: the check box to specify
Gamess-US style z-matrix writing now print a
small explaining message when operated
Fri May 12
- Molden generated Povray orbitals had swapped
colors with respect to VRML and OpenGL orbitals
This is corrected.
(blue = positive, red= negative)
Thu Apr 27
- BIOSYM/MSI car files for non-periodic work again
- In z-matrix editor: instead of "clear status all variables"
you now get the option to set the status to variable
or constant
- In z-matrix editor: Added a check box the specify
Gamess-US style z-matrix writing
- In z-matrix editor: when typing "c" in the main drawing
window molden will look for a file "mapfile" which
contains coordinates to orient cartesian coordinates
after z-matrix -> cartesian conversion
Example "mapfile"
1 50.006 81.343 67.412
2 50.599 80.892 66.194
3 49.514 80.759 65.162
Contains coordinates (angstrom) of atoms numbered 1,2,3
Thu Mar 30
- Molden now nolonger always creates the file 'plot'
The xwindow interfaces doesnt, here you generate
a postscript plotfile by clicking the corresponding button.
Only when supply you molden with a keyword file it will
create the plot file
Thu Mar 23
- Added primitive support for Jaguar cube files
No molecular geometry is displayed however.
Start molden without a filename on the commandline
Go to the density mode, click "Read Cube", chose "Jaguar"
supply a filename, then click the "space" button and supply
a contour value.
Tue Mar 14
- Fred Arnold added support for reading Gamess-us
orbital localisation schemes; Pipek-Mezey and
Edmiston-Ruedenberg
Thu Mar 09
- Changed povray writing didnt work for orbitals,
corrected by Fred Arnold
Wed Mar 08
- Under edit cell parameters, you can now also specify
a spacegroup name, instead of just a spacegroup number.
Fri Mar 03
- support for Gamess-us version with long contraction
coefficients.
Tue Feb 29
- Fred Arnold updated the writing of povray files.
Thu Feb 24
- Molden now nolonger dies when you kill one of its windows
- Added a restore color options, under the color palette
icon
Wed Feb 23
- molden used to center a molecule by working
on the atomic coordinates directly.
Now this is accomplished via a viewing transformation
the coordinates are not affected.
- In principle now the conversion of a z-matrix to
cartesian takes into account the original orientation
of the molecule in cartesian space
Fri Feb 11
- Added writing of CML molecules (primitive)
- With the introduction the new style of rotation
there was a clash between the use of control
for zooming in and for temporarily escaping selecting
of atoms, under the "Reorder Z-matrix" button of the
Z-matrix editor
Wed Feb 02
- Added dynamic memory allocation for reading mopac .gpt
files.
- corrected reading of *.ogl files by moldenogl,
created with mopac .gpt files.
Mon Jan 31
- added commandlineflag to adjust the maximum number
of Gif files molden will write (default 100)
molden -j 2000
Molden will write 2000 files at the max.
Fri Jan 28
- While adding OpenGL support some errors were
introduced for the platforms VMS, CRAY and AIX
Mon Jan 24
- Full support to view orbitals/density etc. in OpenGL
This is accomplished via a helper program called
'moldenogl', this needs to be build separately.
(make moldenogl), you need to place this program
in a directory which is in the default path, say
/usr/local/bin. You can evoke it from the Xwindows
interface under the 'Vr' icon, option OpenGL.
Molden will write a file 'molden.ogl', which will
be read by the helper program. If you want to save
this file you will have to rename it before you
choose OpenGL again. You can run 'moldenogl' standalone.
moldenogl file.ogl
This has been tested for Silicon Graphics and linux.
The latter needs the MESA graphical library
have a look at URL: http://www.mesa3d.org/
You may need to activate the 'LIBSG' line for your
platform.
HOW TO OPERATE MOLDENOGL:
Use the mouse to rotate the scene, drag while holding
down the left mouse button.
Further one letter commands:
Left Mouse button - rotate
Left Mouse button + Shift - translate
Left Mouse button + Control - zoom in / out
Right Mouse button - bring up options
m - toggle molecule
x,y,z,X,Y,Z - move position of light
PS. On linux the mesa libraries are installed in the
the directory /usr/local/lib. This may give the
problem that moldenogl cant find these libraries,
you can remedie this by either copying the libraries
to /usr/lib, or setting the environment variable;
LD_LIBRARY_PATH, in say /etc/csh.cshrc
(setenv LD_LIBRARY_PATH "/usr/lib;/usr/local/lib")
You generate .ogl file from a molden keyword file by use
of the keyword OPENGL.
- added comandline option -t, which will let molden read
chem3d style ascii .gpt files (mopac93)
- added a threshhold for plotting displacement vectors
in the postscript output of a normal mode.
You can set it via the -y commandline flag:
molden -y 2.0
(default the threshhold is 0.0, every arrow is plotted)
Thanks to:
Valentin P. Ananikov
NMR Group
ND Zelinsky Institute of Organic Chemistry
Moscow, Russia
e-mail: val@cacr.ioc.ac.ru
(URL: http://nmr.ioc.ac.ru/Staff/AnanikovVP/molden-t/
PS: the path uses the -t commandline flag, this is now -y)
Thu Jan 13
- The color editor didnt work well on linux, fixed it.
Wed Jan 12
- Added first primitive support for OpenGL,
THE BELOW IS OUTDATED HAVE A LOOK AT THE ENTRY FOR Jan 24
read the makefile on how to activate it.
It only works for Silicon Graphics machines and
linux machines. The latter needs the MESA graphical
library. Currently only a the equivalent of the 3dx mode
is available.
You can only activate the OpenGL via a molden keyword file,
and the use of the keyword 'silly', file 'molin'
Title
file=test/adf.molf silly homo
./molden molin
Use the mouse to rotate the scene, drag while holding
down the left mouse button.
Further one letter commands:
m toggle molecule
. zoom in
, zoom out
x,y,z,X,Y,Z move position of light
- Added the another type of molecular rotation model.
It is available via a new icon in the lower right
corner of the 'Molden Control Window'.
In this model you rotate the molecule by dragging
the mouse while holding down the left mouse button.
Doing the same while keeping the 'Shift' button pressed
lets you translate the molecule.
Doing the same while keeping the 'Control' button pressed
lets you zoom in/out.
Wed Jan 05
- Added maxmimum line width selection under:
the palette icon, the option: 'shade depth'.
Wed Dec 22
- Added depth of shade editor, under the palette icon
there is a new option: 'shade depth'.
This option has no effect on the solid drawing mode
with perspective off, only the stick mode and
solid+perspective modes are affected.
Tue Dec 21
- Added the ability to edit colors, under the palette icon
there is a new option: 'edit colors'. This option will
edit the basic 15 colors available in molden. It will
write the colors toe the file '.moldenrc' in the users
home directory. The use of 'molden -r colorfile' takes
precendence over the reading of .moldenrc.
To reset to the defaults just remove the ~/.moldenrc file
Thu Dec 9
- the WRZMAT keyword now writes the last z-matrix of
say a geometry optimisation, instead of the first
- added the commandline flag '-=', which causes a
gamess-us dialect of gaussian zmatrix to be written,
it has the = sign between variable names and values
For use with COORD=ZMAT
- Gamess-UK6.2 energies of the geometry convergence
were not read properly, fixed it
Wed Dec 08 - Updated the makefile entry for CRAY unicos, for
running the f90 compiler
Thu Dec 02
- writing of non-periodic MSI files used atomic units
rather than angstroms, corrected it.
- When writing postscript in the molecular mode, molden
will check for dummy atoms and will ask you if you
want to include them in the plot. In the current situation
dummies where not plotted.
- In the molecular mode you can change the connectivity
of the atoms, but not so in the density mode. This proved
a problem for people generating VRML orbitals of metal
complexes, i have solved this ONLY for the VRML writing:
Before it will write the VRML molecule, it will check
for the existence of a file called 'molden_connect'
(be sure you have the permission to read it,
ls -l molden_connect), this file should hold the
connectivity of the molecule, per line two number;
atom1 atom2 If atom2 is negative, molden will read an
extra line with 5 numbers it will average the
coordinates of these 5 atoms and create a bond
between atom1 (of the first line) and the average over
the 5 atoms (of line two), it will use the color
associated with the first atom of line two. If you want
to average over less then 5 atoms just supply
zeros for the remaining atoms
(so avg over 3: i1 i2 i3 0 0)
DONT FORGET TO REMOVE OR RENAME THE 'molden_connect' FILE
AFTERWARDS.
- When you select atoms in the Z_matrix to 'cut out' a part
of the atoms to create a new z-matrix, properties like
atoms types, forcefield types, color, residue and charge
are now inherited.
Thu Nov 18
- Added keyword POVRAY, to generate the povray file molden.pov
- Added support for Ampac style cube files
Thu Nov 11 - Fetched some minor problems:
- some msi files were not read correctly, fixed
- gamess-US, sometimes doesnt end coordinates
with an empty line, but with:
'...... END OF ONE-ELECTRON INTEGRALS ......'
dealt with
- the geometry convergence window sometimes didnt
update correctly, fixed it + made them smaller (for PC)
- when moving atoms in a cell you couldt use the
distance button anymore, fixed it
Tue Oct 12 - Solved problem when replacing last amino acid
Thu Oct 7 - Reading msi files generated stray atoms when H-bonds
where present in the msi file, resolved.
Thu Sep 30
- First support for GamessUK6.2, now coping with changed
orbital writeout
- Added Button to the Z-matrix window to make it smaller.
- GLX and ASX PDB residues are mapped to GLN and ASN
GLX and ASX caused problems in protein z-matrices
Mon Sep 20
- fixed bug: when creating a peptide via the z-matrix
closing the z-matrix window and then opening it again
caused molden to crash.
- Added support for MOL2 protein files, small molecules
were already supported.
- Added support for reading/writing MSI Cerius files,
The reading is NOT robust, it will read simple, periodic
structures
Thu Sep 9
Molden now uses dynamic memory allocation for the
size of the grid, this will allow you to read in
any size gaussian or vasp cube files.
It also allows you to redefine the size of the grid
in points from the 'plotplane' window, via the commnds
nptsx= nptsy= nptsz=
Previously the maximum was nptsx=nptsy=nptsz=61
The molden version created with 'make noxwin' is NOT
dynamic.
Mon Sep 6
Molden now uses dynamic memory allocation in some
parts of the program:
- For a z-matrix of a protein
(Not for reading a z-matrix of a protein)
- For basis-sets larger than 256 orbitals
Not done are for instance the maximum size of a grid
(which is 61*61*61), so cube files with larger dimensions
are still a problem
The molden version created with 'make noxwin' is NOT
dynamic.
Mon Aug 23
Linked Z-mat variables were not updated onscreen.
Non bonded atoms in the stick mode were not correctly
shown in the postscript output
Thu Aug 19
A word of WARNING:
Molden3.6 has gone through quite a few
drastic changes, it can therefore be expected to have a few
bugs introduced, so for the time being use this version
at your own risk, and PLEASE report any problems you
encounter (schaft@caos.kun.nl)
- Improved filemanager, it now also works correctly in
directories other that the current.
A directory select window has been added.
- More labels options: added "pdbsymbol","residue"
- Molden now treats any color depth greater or equal 8
as having 256 color cells
- Molden "Author" icon has been replaced by the "FF" icon
which when clicked pops up the ForceField type assign
window. You can still invoke the author window by typing
"a" in the drawing window.
- Typing "u" in the drawing window, brings molden secondary
windows ontop of the drawing window. (This may not work
with the gnome window manager).
- In the stick drawing mode, atoms which are not bonded
used to be invisible, they are now represented as crosses.
- When saving a structure as PDB file it will ask you
if you want to write the Hydrogens or not.
- Under the "H" icon an option has been added to
recalculate the H-bonds.
- The biggest addon is the pdb to z-matrix conversion,
in essence this was already there in the 3.5 version,
but was very buggy (there will probably be some more :-))
In the 3.5 version the whole z-matrix of the protein was
shown, which is way to much and cumbersome to handle.
In 3.6 the default is to create a z-matrix representation
which list the aminoacids with its phi,psi and chi angles.
You can click on the Aminoacid button and choose from a
number of options:
Switch On
Switch Off
Center
Contacts
Delete
Insert
Replace
The one letter codes are also displayed. You can search
with a string of one letter codes. There is a button to
go to the "full Z-matrix"
Unlike the old behaviour, ONLY variables which were changed
on screen are updated in the internally stored z-matrix
IMPORTANT:
MOLDEN WILL ONLY PROMPT YOU TO CREATE A Z-MATRIX
FOR A PDB FILE WHEN IT HAS ENOUGH ROOM TO STORE
THE Z-MATRIX, DEFAULT IT WILL ACCOMODATE 1000 ATOMS,
NOT ENOUGH FOR MOST PROTEINS. SO YOU HAVE TO CREATE
A BIGGER VERSION OF MOLDEN:
- edit the file "change_parameter"
- replace the body:
1,\$s/maxorb=256/maxorb=1024/
1,\$s/numatm=150/numatm=300/
by:
1,\$s/maxat=1000/maxat=20000/
- save this file and execute it:
./change_parameter
- change_parameter only works on the fortran files
you have to edit the C code manually:
- edit xwin.c, replace:
#define MAXAT 1000
by:
#define MAXAT 20000
- save the file, and type 'make'
Molden3.5:
Mon Jul 19
- Fixed bug which let you not save charges you edited,
when you start of with a file which has no charges
Thu Jun 17
- removed small bug in rdgaus.f which made some compilers
stop.
- added the capability to write and read files with custom
spherical atom densities to be used in difference density
plots (bonds keyword).
molden inputfile
inputfile:
some title
file=gaussian_atomic.log genat
a file 'basiinf.mbi' will be written, these can be
concatenated and read back in to molden, fi:
molden -x atomicdens
Thanks to Bjoern Pedersen who implemented it.
(Bjoern Pedersen, Technische Universitaet Muenchen
Institut fuer organische und Biochemie,
Bjoern.Pedersen@ch.tum.de)
Thu Jun 3
- Added resizebility of the geometry convergence window
- Removed SERIOUS BUG introduced Fri May 21
Wed Jun 2 Added commandline opiton -m, which turns off bell sounds
Fri May 21 Added scale factor for normal mode displacement vectors
in the frequencey window.
Fri May 7
GAUSSIAN:
- COMPOUND jobs, (optimisation, followed by a FREQ job)
should now be oke.
- Gaussian98 doesnt print 'input orientation', for a
molecule with more than 50 atoms, in this case molden
couldnt show intermediate structures of an optimisation
run, FIXED. (The problem could be fixed by supplying
IOP(2/11=1) but molden now always takes the 'standard
orientation' and disregards forces (for more than 50 atoms))
Tue Apr 27
- Support for reading Gaussian cube files via the
molden keyword file (new keyword GAUCUB):
tlite
gaucub=test/test_homo.cube space=0.1 vrml
Thu Apr 22
- Molden can write VASP POSCAR files, under the 'cell' icon,
'write' -> 'write VASP', Molden can also read these files
(Use always 'direct or selective' keywords fullout)
(Use the first line not as title but put the element
names in there).
Read support is rudimentary; POSCAR files have all atoms
lying in the cell, which may give a scattered outlook
of the molecule in the cell.
Molden can also read the VASP density grid files, although
they tend to be too big for the default molden version.
Presently only grids which axes are under 90 degrees
will be accepted.
- Changed under the 'Cell' icon: the seperate write options;
'write DMAREL', 'write SHELX', 'write CRYSTAL95', into
one options 'write', which lets you select out these
options + 'write VASP'
Thu Apr 15
- Molden can now generate Gif's for 24-bits displays
Fri Mar 26
- Added Possibility to delete and move atoms in a
crystal, under the CELL icon, the last two options.
It was already possible to translate the atoms in a cell
but this was interactively, the new translate option
allows discrete translations (say 0.5 0 0) of selected
atoms in the assymetric unit.
Fri Mar 5
- Added commandline flag "-geom XXXxYYY-xxx-yyy"
where XXX and YYY are the size of the window in pixels,
and xxx and yyy are the position of the window in pixels.
Thu Mar 4
- Molden can now read Gaussian Cube files:
restrictions:
- these must be formatted cube files
- supported are: density, potential and orbital cubes
(orbital cubes only with ONE orbital!)
- the grid MUST be rectangular
- grid can only be read in the 'density mode'
- Molden now also supports grids which dont have an
equal number of points in all three directions,
and also the radius in the three directions can be
different, under the 'PlotPlane' window there are now
6 new keywords available:
npts1,npts2,npts3 and edx,edy,edz
Molden3.4:
Fri Feb 12
- Added support for G98 optxyz output
- Added support for Pluton SPF format
- Added some aminoacid sequence editing stuff
Tue Jan 19
- Tinker optimisation of structures in molden is done
in the Z-matrix ordering of atoms, even if the read in
structure is a Tinker xyz file. The last case was not
handled properly, it is fixed. You can optimise in the
original ordering by suppressing the generation of a
Z-matrix by using the commandlineflag -a
Tue Jan 12
- Fixed bug in writing chemx .cssr files
- Fixed bug in creating the super cell
- Fixed bug in interpreting molden-format when [5D]
was used.
- Added calculation of electrostatic energy, a new
button 'E q' was added and a field for specifying
the residue number (Eq also calculated interresidue
electrostatics), both in the 'Atom Attributes Window'
this is popped up when you click with the middle
mouse button on a atom.
Shift Mouse click in the residue field lets you set
this residue number to all the atoms you will subsequently
select.
- Added -R npts commandline flag this allows you to
downsize the size of the grid in points.
You can compile with a bigger number of maximum points
(Use the script 'change_parameter':
1,\$s/mx3d=61/mx3d=200/
to change the grid size, memory is a consideration
since an array of the size mx3d*mx3d*mx3d will be used.)
Thanks to:
Bjoern Pedersen
Technische Universitaet Muenchen
Tue Dec 1
- Molden treated Gaussian semi-emirical optimisations
as single points, fixed it
- With Tinker xyz (charmm,amber), the caps are nolonger
(faultily) assigned as residues
Mon Nov 30
- Fixed bug that makes molden crash on WinNT/95 and linux
when a mopac GRAPH file is read and the orbital select
window is activated
Mon Nov 9
- For the submit gaussian job, molden now also looks
for the g98root environment variable.
Tue Oct 20
- support for cssr.arc files.
Tue Oct 13
- Removed bug introduced Sep 23, which disabled the
mapping of files onto the z-matrix
- Further integration of wijnand Mooy's xtinker.
Mon Oct 5
- Removed a bug which would in some cases now
show a structure in the "molecular mode" for
Guassian98 files.
- Implemented tinker "amber" force field
Tue Sep 29
- Removed bug that occured when viewing MO's from MOPAC/VAMP
in the "Molecular Mode" created in the "Density Mode";
the connectivity of the atoms would be messed up.
Mon Sep 28
- Implemented tinker preferences window.
Wed Sep 23
- Implemented, real time structure optimising with
tinker mm3 (small molecule) or tinker charmm (proteins).
the molecular display is updated with the intermediate
structures. At the end a tinker archive file is created.
- Support for tinker archive files.
- Vrml from the elctrostatic potential derived from charges
in the density mode, now shows both positive and negative
lobes.
- Adding of fragments can now be done at the start of a
new z-matrix
Fri Sep 18 - In submit job (Gaussian, Gamess) the check for charge
and multiplicity gave an error when there was an dummy (X)
present.
Mon Sep 7 - Added VRML equivalent of the 3D-X plotting mode,
first select this mode from the Molden Control Window,
then click the "Vr" icon.
- Added creation of peptides.
Click "ZMAT Editor", select "Substitute atom by Fragment",
select "Sequence" and the "Build Sequence Window" will
pop up. Select what kind of conformation you want; alfa
helix, or beta (sheet) alternatively a turn. This selects
the PHI and PSI angles used. You can still change them
in the corresponding PSI and PHI fields. Now specify an
amino acid sequence by clicking on the residue buttons,
a status bar shows the last 16 residues selected.
You can correct an error with the "Undo" button.
When ready click "Build".
Alternatively you can read in a protein file, which should
contain per line:
'3 letter amino acid code' Phi Psi [Omega] [Chi1] [Chi2]
[Chi3] [Chi4]
Everything between [] is optional.
The files used by tinker to create peptide can be used.
Molden will remember the last amino acid added, so that
new partial sequences can be added without selecting an
atom to which it should be attached.
When ready you can write it out as a PDB file, in the
"Molden Control" window click "write" select "PDB".
You can also write it as a tinker charm file, close the
ZMAT-editor, click with the middle mouse button on an atom
this will bring up the "Atom Attributes Window", click on
The Force Field button and select "Tinker Charmm", now click
on the write button int the "molden Control" window and
select "Tinker".
Tue Aug 25
- Fixed bug that let molden crash on certain pdb, tinker
charmm files.
Tue Aug 11
- Added support for Gaussian98
- Molden now adds hydrogens to the amino acids and
nucleotides of a PDB entry.
- Added checking to user selection of atom types,
for Tinker MM3 aand Tinker Charmm.
Molden3.3:
Thu Jul 23 - Added actinide elements, to atoms property editor
- Fixed small bug which wrongly switch label button
when FFtype was selected.
Wed Jul 22 - Fixed bug in code to deal with ADF orbitals
(Fabio Mariotti)
- Gamess-uk/us uses different sequence of F orbitals
than gaussian, molden always did the gaussian way,
corrected.
Mon Jul 20
- Fixed small bug which prints lots of arrows on a molcular
postscript plot when normal coordinates are available.
- the ADF routine assumed exponents and normalisation
constants read in from a molden format file as written
by the ADFrom program to be in atomic units, this was
not the case, the routine has been adapted.
Tue Jul 14
- By default molden always tries to make a z-matrix if
there is none, occasionally it will have to add a
dummy atom to accomplish this. This could cause
problems reading some of the frequencies of a frequency
job. Noe Fixed.
Mon Jul 13
- The window that lets you edit forcefield types,
is now brought up when you select the label "ForceF.Type"
When you click an atom with the middle mouse button
as before this window is also popped up, but in addition
the labelling is set to "ForceF.Type"
- When using "Optimise" from the z-matrix editor it
checks wether atoms typing has already been done.
- Added some tinker forcefield parameters for acids, and esters
to the .key file written when selecting "Optimise with Tinker"
Wed Jul 8
- Added almost all spacegroups.
- for molecules with no crystal information, it will
be generated when you click on the CELL icon
- Added reading of biosym arc files, use the movie
and next button in combination with the "Geom. Conv."
button.
- Under the CELL icon, option "edit cell parameters";
you can now change the spacegroup of the cell
- FDAT files containing multiple entries can now
be viewed with the "Next" button.
- Added "fit multipoles" under the surface icon
(molden has to be compiled with "make molden.mpfit"
for this option)
- Added "Optimise xtinker" option under the CELL icon
this writes input files for and executes an adapted version
of xtalmin, an crystal structure optimiser from the tinker
suite of programs. Adaptation by Wijnand Mooij, not yet
available in the tinker distribution.
Mon Jun 15 - Added plotting of distance monitors to postscript
- Added more types for tinker mm3, automatic assigning
still restricted to the old types.
Thu Jun 11 - Added writing of Chemx(CSSR) files.
IMPORTANT !!!!!!!
- Fixed BUG in reading GAUSSIAN94 frequency outputs.
It was introduced on 11 april 1998.
Wed Jun 3 - Added Scrollable scrollbars
- Added atom dynamic typing, click with the middle
mouse button on a atom.
Tue May 19 - Fixed a bug in molden.f which caused some compilers
not to compile it. (Introduced at Thu May 14)
- Writing of animated vibrations in VRML2.0:
molden -w3 test/mopac.freq
Click "Norm. Mode" button, select a frequency, say 11
a file "freq11.wrl" will have been written now.
Thu May 14 - Added routine to fit multipoles to the electrostatic
potential, stuff written by Wijnand Mooij
(w.t.m.mooij@chem.ruu.nl), use keyword 'MPFIT'
together with keywords described in file 'mpolefit.f'
type 'make molden.mpfit' in the source directory to
add this feature to molden.
- The new Gamess-US prints frequencies a little different
which caused molden not to display the right frequencies
this is solved
Wed May 6
- Milan Hodoscek (xvibs) supplied code to plot
normal coordinates as arrows in the postscript
plot. EG: molden test/gaussian.freq
click on Norm. mode button, choose the frequency,
then click on Norm. mode button again, now click the
postscript button. You can use the -s commandline flag
to scale the amplitudes (eg: molden -s4.0)
Mon Apr 27
- Improved the writing of VRML2.0 animations.
These are invoked by:
molden -w3 geometriesfile
Then clicking the "Movie" button. At completion
the VRML2.0 file 'movie.wrl' is written.
It include a file via the WEB:
http://www.caos.kun.nl/~schaft/molden/wrl/animator.wrl
You can edit the movie.wrl via and subtitute the
EXTERNPROTO declaration by the contents of animator.wrl.
Other adjustable parameters are the size of the animation
window: Window [2,1] (Within the DEF MOLDEN_ANIMATOR
definition). The cycleInterval in DEF MOLDEN_TIMER
this is the time the animation should take.
Wed Apr 15
- Added possibility to 'read' and 'write' basis set
3D grids, a file 3dgridfile is created.
- Added choice of solid molecule draw:
"molden radii" (The old molden solid)
"vdwaals radii"
This on user requests.
Tue Apr 14
- Added reading of BOYS localised orbitals for Gamess-US
Fri Apr 3
- The non Xwindows version of molden now works again
- Crystal visualisation support for chemx .cssr format
and biosym .car files
- Through the Z-matrix editor you can build z-matrices
which have translation or screw-axis symmetry.
Read in the repeating unit, then click on
"Substitute atom by Fragment"
pick "Periodic", pick "Translation" or "screw-axis",
specify the number of repeats.
Mon Mar 23
- Support for the new(?) gamess_us PC version is
has been added.
- Added animation of z-matrix variables.
- Added writing of POVRAY files
Fri Feb 13
- enabled atonnumbering in postscript printing
- Electrostatic potential mapped to an isodensity
surface is now possible. Also charges derived this way.
- Writing and reading of surfaces.
- Orbitals can be displayed as surfaces as well
Tue Jan 27
- Enabled writing of 'ATOM' records in the PDB
format.
- Enabled writing of Tinker Charmm files
- Postscript files written by molden, now allow
the turning of of the zero contour
- Molden Postscript supports non solids drawings and
shading on these sticks
Fri Jan 9
- Added posibility to create a super cell
- Added read/write support for the crystallographic
SHELX format (LATT 3, not yet supported)
Thu Jan 8
- Constants read in from the constants section of a
gaussian/gamess-uk input file are flagged as such
in the z-matrix editor, constants which have other
variables linked to it, are written to the constants
section of an gaussian/gamess z-matrix
Wed Jan 7
- Fixed small bug in the gaussian output reading routine.
When reading frequency output and encountering a
'exceeding maxnum of orbitals' condition, the wrong
coordinates were read.
Fri Dec 5
- You can now specify the order of atoms in which a
Z-matrix is to be created
- When working with files which contain crystal information
(FDAT,MOL2,MSF) it is possible to map a z-matrix on file
onto the cartesian coordinates. Your z-matrix file has
to contain extra mapping information, so after the
Z-matrix itself you have to supply the keyword 'map'
followed a line per z-matrix atom which indicates
to which atom it corresponds in the cartesian file.
The name of this special Z-matrix file has to be 'mapfile'.
You then start molden with the commanline flag -Z:
molden -Z test.fdat
Mon Nov 24
- removed bug introduced a week ago, that messed up the
connolly surfaces
- Added distance monitors
- Added editing of cell parameters.
- Added the possibilty to align two structures:
Read in stucture 1.
Click the align icon in the center of the molden control
window. Then supply the filename of the file containing
structure2. Now use the standard ways of rotation,translation
and zoom in/out (z-translation) to align stucture2 to
structure1. You can also use the origin icon to change
the center of rotation in structure2.
You can switch between rotating both structures or
structure2 by using the Esc key.
Use the Tab key to align by selecting three couples of
atoms (a couple = atom structure1 (red), atom structure2
(white)
- Reading Support for the tinker .xyz format (mm3/charmm)
- It is now possible to work with crystals and change
the position and orientation of the packed molecuul
via the "Cell Rot On/Off" option under the cell icon.
You can switch between rotating both structures or
structure2 by using the Esc key.
At the same time you can change the packed molecule itself
via the z-matrix editor.
- Molden can now write input files for the Crystal95
package. Basis sets of previous read in gamess/gaussian
jobs are transferred to the Crystal95 input.
Works of course only on fdat files and mol2/msf files
containing crystal structures.
- molden -f pdbfile
would create connectivity from scratch, however the
HETATM records where not dealt with correctly.
- You can change 14 of the colors of the color palette
"molden -r colorfile", where colorfile could be:
atom color(1-15) VandeWaalsRadius, (- = skip)
background color(1-15)
palette red #CF54FD ... (14 colors)
You can continue the last line on the next line when using
the "\" character. You can use color names or Hex red-green
-blue triplets
Wed Nov 5
- Added more spacegroups for use with mol2/msf files.
(100 spacegroups supported)
- Improved crystal building code
- Support for Gamess-US IRC files
- Electrostatic potential due to point charges can
be calculated/displayed on a connolly surface
See Surface icon.
- On mopac output the ESP charges are read in when available.
- Writing of simple pdb files, via the 'HETATM' record.
- Fixed a bug that caused variable names such as 'e1', 'd1'
in a z-matrix input to be not handled correctly.
Bug was introduced with the introduction of the molden format.
Mon Oct 27 - Introduction of the molden_format
- fix of molden format on linux
Molden3.2:
Fri Oct 24 - Introduction of the molden_format, have a look at
the "write" button.
- Normal modes with a sequence number greater than 99
where not handled correctly
- The background color can be set via the molden -r
flag, see molden -h; molden -r
Mon Oct 13 - Gaussian Beta Orbitals were not always visible
specially when read of a checkpoint file:
Fri Oct 10 - Support for ADF, an intermediate program which
reads ADF's tape21 can produce files readable
by molden. This program was developed by Fabio Mariotti
from Prof. Alessandro Bencini group in florence.
This intermediate program will eventually become part
of the molden distribution, but since it is still
under development, you should contact Prof. Bencini:
Prof. Alessandro Bencini
Universita di Firenze
Dipartimento di Chimica, Via Maragliano 75/77
50144 Firenze, Italia
Tel: 39-(0)55-354841
e-mail: sandro@chim1.unifi.it
bencini@dada.it
Wed Oct 8 - Fixed bug in Gamess-UK submit job scheme, the
proper 'vectors' option was not always chosen.
- The Postscript color of the unit cell is now black
per default, it can be changed by in the postscript
file by setting /cellcol
Wed Sep 24 - Added spin density for UHF calculations
Use keyword SPINDENS together with IPSI=0
- Improved dmarel interface
- Removed multiple expose events on the zmatrix editor
Mon Sep 8
- more Gamess-UK version 6.0 support
Fri Sep 5
- removed bug introduced day earlier, resulting
in an floating exception on at least Linux
Wed Sep 3
- Gamess-UK version 6.0, added first support.
- Adapted postscript driver to handle editing of
atom display radii.
Thu Aug 28 - Enhanced atom color editor to atom property editor
Now color, vdw and display radii can be altered.
Thu Aug 21
- Added Submitting of Gamess-UK Jobs.
GAMESS_ROOT has to be set and the 'rungamess' script
must be operational.
Mon Aug 18
- Added atom color editor.
Fri Aug 15
- Removed bug which when molden was started without
a file name would cause the molden control window
to never pop up, certainly on AIX.
- Gamess-US: when using print options to print
'AO MULLIKEN POPULATIONS IN EACH MOLECULAR ORBITAL'
molden didnt read the occupancies correctly,
resulting in the density to be calculated to low,
and mulliken charges to be incorrect, orbitals ok.
Fixed it.
- Added Submitting of Mopac Jobs, still very primitive.
MOPAC_ROOT has to be set
Mon Aug 11 - Removed small bug whith respect to the PLANE/ROT
versus LINE/CENTER keywords.
Using the PLANE keyword the orientation of the calculated
rectangle of points is such that, the first atom specified
with the PLANE keyword together with the center of the
plot lie parallel with Y-plot axis, when LINE/CENTER
or even ROT is used this scheme is abandoned.
Wed Jul 23 - Added Submitting of Gaussian Jobs, still very primitive.
Thu Jul 17 - Fixed bug that was dormant but became serious
on a few platforms after introducing reading of mol2
file on July 13. Files would not be correctly recognized.
Wed Jul 16 - Added writing of tinker .xyz files.
- Added under "XYZ->curr.zmat" in the Z-matrix editor
the possibility to optimise a structure with, sybyl
quanta or tinker.
The corresponding environment variable has to be set
first (TA_ROOT, QNT_ROOT or TNK_ROOT)
TNK_ROOT is not used by tinker itself, but molden needs
it. (eg: setenv TNK_ROOT /compchem/tinker)
The mm3 tinker parameter set will be used.
Running quanta is shakey.
- Removed a bug that applied to Z-matrices automatically
generated for XYZ files, changing variables in the Z-matrix
would screw up the molecule.
Fri Jul 4 - Added writing of Quanta/Charmm MSF files.
- Added atom row containing AG etc. in z-matrix editor.
Tue Jul 1 - Added reading of Quanta/Charmm MSF files.
- You can now optimise you molecule with sybyl
from the z-matrix editor. The environment variable
TA_ROOT has to be set first. Choose the "XYZ->curr. zmat"
button.
Wed Jun 25 - Removed two bugs by which seemingly only the
OpenVMS version was affected.
Mon Jun 23 - The tolerence for partioning multipole expansion
in symmetric molecules was to low, leading very
occasionally to wrong multipoles, for higly symmetric
molecules. Fixed it.
Fri Jun 13 - Incorporated reading and writing mol2 files.
For protein just coordinates are read.
Writing of Mol2 is very primitive, with respect to
atom types, and type of bonds is always single.
But you can convert fdat to mol2 files this way,
including charges, just first calculate charges on
a job with the same atom order as the fdat file,
then read in the fdat file and write mol2 (you will
find it under the z-matrix editor, cartesian coordinates.
Only the top-ten spacegroups have been incorporated,
so 90 % of crystal structures will be read.
Wed Jun 4 - Fixed bug introduced Fri May 30, affecting the proper
writing of zmatrices.
- Fixed also some bug related with "delete line" in the
z-matrix editor, having to do with maintaining the right
status of an internal variable(=constant,=variable,=linked)
- In mopac DRC calculations the potential energy is now
picked up.
Fri May 30 - Rotation around the z-axis is now possible in both
directions, clicking the mouse in the middle of the
screen will give positive rotation, doing the same
while holding down the Control or Shift key will
give negative rotation
- Molden now supports writing of VRML2.0.
Apart from the keyword VRML you can now use VRML2.0
The -W commandline flag does the same.
The various VRML buttons now let you choose between
VRML1.0 and VRML2.0.
The -w commandline flag now knows an option 3.
When the movie button is pressed a VRML2.0 animation
is written (movie.wrl). This can be viewed with a VRML2.0
compliant browser such as Silicon Graphics Cosmoplayer
plug-in (free available, also fro PC's). Clicking on
the molecule will start the animation.
- typing "g" in the display screen will let you read in
and XYZ file which will be mapped onto the current
z-matrix, provided the number and the order of the elements
is the same in both.
Tue May 27 - Added interactive choice between mono and color postscript
Fri May 23 - Added Pasting of strings capability to query boxes
(For now button 3 will do this)
- The interactive calculations of:
True ESP derived charges (Very Slow)
DMA esp derived charges
Mulliken Charges
Via the Surface button.
Thu May 22 - Removed a small bug in calculating the multipole
derived electrostatic potential
Fri May 16 - Charges are printed in postscript when the label
"atom+charge" is active
Wed May 14 - VRML of the elctrostatic potential "space" plots
are now handled correctly.
Tue May 6 - The Z-matrix scrollbar can now be clicked it, it
will trigger pageup or pagedown movement.
Fri May 2 - electrostatic potential on a connolly surface:
When clicking on the color level rectangle in the
upper right corner with the second (or middle) mouse
button you can change the colors used.
- Added keyword DMACH to calculate charges fit to
Distributed Multipole Derived electrostatic potential.
Tue Apr 29 - the true or multipole derived electrostatic potential
on a connolly surface via keyword file now includes a
postscript plot (-C to generate color postscript):
molden -C molin > molden.out
For the true electrostatic potential:
molin:
----------------------------------------------------------
title
file=test/gamess_us.h2o_631g_opt.out postscript vdws elpot
----------------------------------------------------
The new keywords XANG,YANG and ZANG controls the
orientation viewed, usage XANG=45 (45 degrees)
- added the EST parameter set for writing input for the DMAREL
program. (molden -e)
- added a button "H" to undisplay hydrogens, this is handy
in combination with the CSD fdat files when displaying
multiple cells. Getting rid of the hydrogen gives a
clearer view of the crystal packing
- Dummy atoms will no longer be displayed in postscript
molecule plots.
Thu Mar 13 - Molden could already calculate the true or multipole
derived electrostatic potential on a connolly surface,
also VRML could be generated for this but only
interactively, this can now be done with keywords:
molden molin > molden.out
For the true electrostatic potential:
molin:
----------------------------------------------------------
title
file=test/gamess_us.h2o_631g_opt.out vrml vdws elpot
----------------------------------------------------
For the multipole derived electrostatic potential:
molin:
----------------------------------------------------------
title
file=test/gamess_us.h2o_631g_opt.out vrml vdws
----------------------------------------------------------
A file molden.wrl will be written.
Wed Mar 12 - Added ability to display a cell with an Xmol xyz
cartesian file:
After regular atoms add cell points, valid
labels:
OO,OA,OB,OC,AB,BC,AC,ZZ
These cell points must be included in the number
of atoms.
- The geometry convergence window together with
the movie button have been updated:
You can now stop a movie by clicking "first", "next"
or by selecting a point in the geometry window.
The tick marks are adapted so as not to overlap
when there are a large number of points.
- added a file epint.f.g77, gnu fortran has problems
compiling the original epint.f. So before typing
"make", copy epint.f.g77 to epint.f.
- Linux2.* has problems with Molden (And Gaussian94)
this probably due to an operating system bug affecting
memory management.
- Removed bug in calculating the q31s octupole moment
(Only when using D-functions)
- Added commandline flag to keep the order of atoms
when creating a z-matrix from cartesian coordinates
molden -A
- Molden now writes an file "esp.xyz" when doing an
ESP charges calculation, it contains the atoms +charge
in xyz-coordinates
- added support for Gamess-UK rhf localised orbitals.
- Added beta-test support for DMAREL, a package that
can calculate lattice energies from a multipole
expansion.
New Commandline flags:
-E DMAREL input: use coordinates from multipoles
-i opt fdat files:
opt=1 standardise H-C, H-N
opt=2 1 + standardise phenyl rings
Other Relevant flags:
-A Keep order of atoms when creating a Z-matrix
-D opt DMA mode:
0 = atomic sites only (default)
1 = atomic+halfway-bond sites
When creating a z-matrix for an optimisation run to be used
with DMAREL you must keep the order of the atoms as in the
CSD FDAT file and turn of symmetry to keep it this way:
molden -A -i 2 azijnzuur.fdat -> azijnzuur.zmat
To use the optimised coordinates instead of the FDAT
coordinates in writing DMAREL input, use
molden -E azijnzuur_opt.out azijnzuur.fdat
if you want to use bondcenters as well,
molden -E -D 1 azijnzuur_opt.out azijnzuur.fdat
If you want to use fdat coordinates with bondcenters,
molden -D 1 -i 2 azijnzuur.out azijnzuur.fdat
In molden click on the surface button, choose
"Multipole Derived", then read in the FDAT file,
click on the "Cell" button and choose "Write DMAREL"
a file "dmain" will be created.
Wed Feb 12 - In the density mode you could zoom in on the plot
with the second mouse button, sometimes old plot
were mixed with new plots, fixed it.
Tue Feb 11 - GAMESS-US: when using the HSSEND keyword to do a
normal vibration analysis at the end of a geometry
optimisation, the default is to display geometry
optimisation information, but molden -H will
trigger visualisation of normal vibration analysis.
- GAMESS-US: when imaginairy frequencies were present
molden would skip the rest of the normal modes in
that line of the output.
Mon Feb 10 - Fixed bug in the 'space' mode of orbital plotting
A space plot consists of the density/orbital-amplitude
plotting and the plotting of the molecule in the
stick mode. If the density/orbital-amplitude was to low
in a slice then also the part of the molecule in this
slice was not plotted. (This did not affect the VRML
space filling plots)
Wed Dec 18 - Incorporated writing of inputfiles for aresp:
Using the keyword 'aresp' will let molden write
the files 'resp.in' and 'esp.in'
Example keyword file:
line1: test esp
line2: file = water.out espch debug aresp
- The keyword occu dint work correctly, fixed
Wed Dec 11
- Molden can now do gaussian natural orbitals as generated
by the keywords:
pop=(naturalorbitals) gfinput iop(6/7=3)
- Molden with Gaussian94 and outputs with only cartesian
coordinates would say 'reference to an undefined center'
but would still work correct, solved
Mon Dec 9 - Molden didnt recognise certain Gaussian94 UHF jobs.
Resulting in only one set of orbitals being displayed
- Dihedrals with a negative value where not properly
written as constants in write zmatrix
- In zmatrix editor in the line drawing plot mode
the molecule become invisible after adding line two
this because th view direction was along the axis of the
molecule, fixed it.
- some mopac output reads would hang
- added a little more control over the postscript file
Fri Oct 18 Removed following bugs:
- GAMESS-US input files with zmatrix and point group C1
failed
- PDB file containing only non-protein and non-rna werent
handled well
- FDAT files with NRAD=0 failed
Thu Oct 17 Removed following bug, when building a structure
with the zmatrix editor the display would show the mirror
image of the real structure. When writing out this structure
and then reading it back in to molden the structure would
be displayed in the right way.
Wed Oct 9 Added the possibility to do a Distributed Multipole Analysis
and the calculation of Mulliken charges.
For now, Mulliken charges are calculated only for single point
Gamess/Gaussian runs.
The Distributed Multipole Analysis can be activated by use
of the keyword "MOLPOT". Interactively it can be activated
either from the "molden control window" by pushing the
"surface button" (The 6th icon in the middle of the window)
or pushing the "Dens. Mode" button and consequently choosing
the plot function "Elec. Pot" in both cases the user is then
presented with the choice between the true electrostatic
potential and the electrostatic potential derived from a
Multipole expansion. The latter is an order of a magnitude
faster than the first.
Three types of DMA are available, they can be selected via
the "-D opt" commandline flag, where opt can have the values:
0 = atomic sites only (default)
1 = atomic+halfway-bond sites
2 = no shift of overlap dens. of conn. atoms
NOTE: In previous versions the keyword "MOLPOT" was used
with a DMA analysis read from a Gamess-UK outputfile.
Use keyword "RDMULT" to get the old functionality.
Molden3.1:
Thu Aug 29 Calculating the Laplacian via a keyword file, core dumped
It has been resolved.
Thu Aug 22 - When visualizing csd fdat files in the "multiple cells"
problems arose when there were Hydrogen bonds present.
This has been resolved.
Wed Aug 21 - Support for the laplacian of the electron density,
(the trace of the hessian).
Two commandline flags were introduced to aid the
space type of plots with the laplacian.
-L display both neg. and pos. contour in space
plot of the laplacian. Default only the value
specified with "space=value" will be rendered.
-1 use only the lower half of the cubic grid
used for the space type plot
-2 use only the upper half of the cubic grid
used for the space type plot
The latter two were introduced to increase the visibility
of the inner (enclosed by other surfaces) surfaces.
Thu Jul 25 - Corrected a bug which made you have to click buttons
twice
Fri Jul 12 - Corrected problem with postscript
- Electrostatic potential on connolly surface added.
Activated by Clicking on the appropriate icon in the
middle of the molden control window.
Clicking on points of the surface brings of a popup
window with its electrostatic potential value.
In the upper right corner of the screen there is a
color code rectangle, clicking in it lets you change
the increment value between different colors.
The 'molden -G 0.5' commandline flag controls the
spacing between the lines that make up the connolly
surface.
- Added the capability to write VRML
(molden -V filename, specifies density VRML file,
default: molden.wrl)
- You can now create a Z-matrix with symmetry, use
mouse button two in the zmatrix editor, to:
- link variables
- to make constants
- to mark or unmark
Molden3.0:
Thu May 23 - Corrected problems on some platforms with the fdat format
and the reading of XYZ format without the -X flag
Wed May 22 - Rotation in the density window is now attached to button
one, rotation will proceed until the button is released,
cropping is now attached to button two
Wed May 15 - Molden now also recognizes XYZ format without the -X flag
- zoom in/out will proceed untill the button is released
Fri May 10 - Better encapsulated postscript
- Better hydrogen bond display for PDB files
- support for hydrogens on RNA/DNA pdb.
- molden -r fname: read file with per line;
atom color(1-15) VandeWaalsRadius, (- = skip)
- molden -w opt: write all points of a movie to a file:
opt specifies format; xyz(=1) zmat(=2,mopac)
Thu Apr 25 - Increased support for CSD .fdat files.
Wed Apr 17 - Support for mopac93/6.0 irc output
- gamess-uk inputfiles with no variables/constants oke now
- added command line flag for switching off automatic
cartesian -> zmatrix conversion; "molden -a"
Tue Apr 09 - Some platforms dont support the "logical*1"
- Enhanced cartesian -> Z-matrix conversion
Tue Mar 29 - Support for mopac6.0/7.0 force runs.
- Allow to set the background color, via palette icon.
Tue Mar 28 - Support for CSD .fdat files, molden -S will generate
symmetry positions and a unit cell.
- xmol files that used scientific notation (1.0e05)
are now also handled well
Tue Mar 19 Mopac input files didnt show up in the z-matrix editor
fixed it. You read mopac input files as fragment in the
z-matrix editor.
Fri Mar 15 Added built in GIF writing capability, dropping the use
of the external "convert" program from ImageMagick
Wed Mar 13 Extended and improved the rotation of the molecule,
holding the mouse button down in the center of the graph
will invoke rotation around a z-axis
Tue Mar 5 A VERY serious bug effected the calculation of the
electrostatic potential and esp charges with Gamess-US/UK
output. (It was introduced with Gamess-US support nov. 95)
esp's from Gaussian were unaffected !!
- ESP charges: introduced keywords AXIS-X,AXIS-Y,AXIS-Z
They the define the principle axis used in constructing
the atomspheres which make up the connolly surface.
Sometimes necessary when you want to reproduce symmetry.
Wed Mar 4 - support now for dih, -dih variable use when reading
Gamess/Gaussian inputfiles.
- With Gamess-UK optimise jobs molden would show
orbital energies of the first point, instead of the last
point, fixed.
Mon Feb 26 A number of bug fixes and new features, see also
The history of molden2.9:
- Added color postscript for Density Display.
Triggered by commandline flag -C
- Removed bug that would mess up the EUCLID display
when clicking the Postscript button.
- considerably enhanced reading and displaying of PDB
structures.
Helix, beta secondary structure information, will
by default be read from the PDB file, if not available
Molden will calculate secondary structure information.
Use "molden -g" to allways force the latter.
From the "Residue Command" window this information can
be edited.
The color postscript rendering of PDB structures has
also been dramatically improved.
Molden also lets you display parts of the molecule as
a connolly surface.
- molden now supports pure F/D-functions (7f,5d)
- GAUSSIAN: molden now also read orbitals from dft
calculations.
- Added commandline flag -h, which prints the available
options.
Molden2.9:
Thu Feb 22 - Added color postscript for Density Display.
Triggered by commandline flag -C
- Removed bug that would mess up the EUCLID display
when clicking the Postscript button.
- Made postscript file more suitable for customizing.
Tue Feb 20 GAUSSIAN: molden now supports pure F-functions (7f)
molden only used to read cartesian F (10f)
(As with pure D, not yet for the electrostatic
potential)
With Gaussian92 and older in combination with
ROHF all orbitals were printed, Molden now
reads all the orbitals.
Fri Feb 16 GAUSSIAN: the use of nosymm could lead to problems.
Think I've tackled it now.
Also the SCF convergence reading when
"SCF Done: E(RB+HF-LYP)" was on the output
could cause problems.
Thu Feb 15 Changed default to Color Postscript for the molecular
display. (Color postscript for the density display not
yet implemented) Mono postscript can still be generated
by use of the commandline flag -M (molden -M)
Thu Feb 8 - Removed bug in postscript printing.
- PDB: default is now to read secondary structure info
from the PDB file, if there is non the info is
calculated. Use "molden -g" to allways force the
latter.
Wed Feb 7 The postscript (color) rendering of protein structures from
the PDB has considerably been enhanced
Fri Feb 2 Removed small bug affecting only Ultrix versions of molden
when displaying dummy atoms in the solid mode.
Removed small bug affecting Ultrix,Solaris when adding
a fragment in the Z-matrix editor when no line is selected
Thu Feb 1 On the rs6000 (ibm,aix) molden sometimes gave annoying
run time warnings, such as "C invalid decimal digit"
Wed Jan 31 - GAMESS-US:
With geometry optimisations, for each geometry point
the z-matrix is read from the output. It used to be
generated by Molden. To update the coordinates on screen
with the coordinates belonging to the z-matrix,
push "Aplly current changes to Z-matrix"
Supplying "molden -u" will restore the old behaviour.
- Removed small bug which caused problems on
a Gaussian optimise job on an already optimised
geometry (vectors are still a problem in this case)
Tue Jan 30 - Added connolly surface's for protein (PDB) viewing.
- Added commandline flag to scale normal motions
molden -s4
will increase the amplitude of the vibrations times 4
Molden2.8:
Tue Jan 25 - Removed small bug in the automatic z-matrix generation
- GAMESS-US: not converged optimisations showed a last
invalid point, rendering de energy plot useless.
- Problems encountered when having more than 200 points
in an optimisation or IRC have been dealt with.
Tue Jan 23 Gaussian: molden used to generate its own z-matrix
for the z-matrix editor (except gaussian input files)
Now it retains the z-matrix on the outputfile.
(except for "force jobs")
Tue Jan 22 Removed small bug in displaying SCF convergence, SCF
convergence of last point sometimes not displayed.
Thu Jan 18 Provisionally supported gaussian 5d functions.
(density only, electrostatic potentials not yet supported)
Wed Jan 17 Removed a bug affecting the reading of gamess input files.
Wed Jan 16 Added beta sheet solid rendering.
Fri Jan 12 Added numbering to atoms on screen for the convenience
of the Z-matrix editor (switch on label when in the
zmat editor.
Added "substitute atom by fragment" capability in the
zmat editor, you can also read a gamess/gaussian/mopac
input file as fragment.
1995
Thu Dec 21 Added nucleotide support when reading PDB files
Thu Dec 20 Removed bug in z-matrix editor which yielded
wrong guesses for bond distances for rare atoms
Removed bug in z-matrix editor, which in case of a wrongly
user supplied value and when the # of zmat lines was less
than 9, would garble the zmat-editor screen.
Thu Dec 7 Removed a bug which only affected the Sun solaris version.
(In the z-matrix editor whilst adding the second atom)
Tue Dec 5 MAJOR BUG FIXES:
- molden with GAUSSIAN94 UHF showed only alpha orbitals
- GAMESS-US UHF geometry optimisation showed no orbitals
Thu Nov 30 removed sleep call in inferr.f, caused problems on AIX,linux
and openvms.
Zmatrix editor now supplies the first fragments
Wed Nov 29 On AIX molden hangs after pushing the "space" button,
it was caused by a call to sleep, which should return
after 2 seconds but it never returns, you have to
deactivate this line in file inferr.f
GAMESS-US IMPORTANT BUGS:
- Scf-Convergence of GAMESS-US outputs would be empty
when "* * * INITIATING DIIS PROCEDURE * * *"
was on the output. Taken care of.
- fixed inproper reading of orbital occupancies.
- fixed incorrect handling of normal vibrations > 9
Tue Nov 21 When entering the z-matix editor without having read a file
first, an error occured while adding the second atom of a
new z-matrix, removed it.
Cleaned up z-matrix editor code for monochrome displays.
Removed a bug in routine hidedr, only OpenVMS affected.
` Z-mat editor is a little more intelligent now.
Fri Nov 10 Protein viewing: removed inconsistency in displaying hetatm
records
Mon Nov 6 Gaussian-94 users NOW should use iop(6/7=3) instead of
iop(6/7=1), the latter option under g94 nolonger prints all
occupied orbitals, the first prints all orbitals.
Fri Oct 20 First beta support for Gamess-US
And both alpha and beta orbitals (UHF runs) are now displayable.
Molden2.7:
Mon Oct 9 Made minor changes to let the code compile on Linux,
the user has to edit file inferr.f before compilation.
Thu Sep 28 The distance,angle and dihedral button now display their
output in a dedicated window.
Wed Sep 27 Support of Gaussian94 output.
Fixed bug introduced on Sep 11, which made the gamess
vibration animation routines use the wrong set of coordinates.
Molden2.6:
Tue Sep 26 Support for pdb ambiguity amino acids, asx,glx,his
and hydroxyproline (hyp).
Also HETATM A.. are now recognised.
Added popup box that lets you choose the color of your HETATM
molecule.
Fri Sep 22 Fixed an important bug introduced on Mon Sep 18.
Mon Sep 18 The cartesian coordinates to z-mat converter now WILL
produce a z-matrix for molecules containing 3 atoms on a line.
Fri Sep 15 Added the capability to write cartesian coordinates from
the Z-matrix editor.
Thu Sep 14 Fixed a bug that lets molden crash on some systems, in the
case of a molecule containing 3 atoms on a line.
Fixed a few other unclarities in the z-mat editor, however
the z-mat editor still needs a lot of work.
The cartesian coordinates to z-mat converter will not
produce a z-matrix for molecules containing 3 atoms on a line
Mon Sep 11 Single point gamess calculations retain their user specified
z-matrix in the z-matrix editor
Thu Sep 7 For pdb files only:
Made second display type for the solid helix default
Added "neigh=r" command in the residu command window.
Neigh looks for neighbours at distance r
Changed "substrate" to "hetatm" in the molden control
window, clicking it will lets you choose which hetatm molecules
you want to display
Tue Aug 1 Added second display type for the solid helix
Mon Jul 24 Display of vibrations for mopac (tested on mopac93)
Fri Jul 14 Incorporated calculation of charges fitted to the
ElectroStatic Potential (ESP) on a series of connolly
surfaces. (Only for gamess/gaussian) (see test/esp.txt)
Molden2.5:
Fri Jun 30 The compilation of xwin.c caused some problems on non-ansi
compiler systems (hp,sun), fixed it.
Thu Jan 26 Removed redundant code which made molden eat cpu when it
should be idle.
Apparently molden plotted inverted molecules, changed it
Jan Improved lighting (At least for protein viewing)
1994
Fri Oct 21 Made support for XMOL cartesian format. Use -X flag
Thu Oct 20 Changed resolution of postscript molecule plotting,
depending on number of atoms. (Plotting proteins was
very slow)
Eliminated trailing in rotating the molecule.
Molden can now generate color postscript for the molecule
display by using the -C flag.
Tue Sep 22 ZMatrix editor implemented, incorporating a very rudimentary
builder.
Molden2.4:
Tue Aug 16 Scf/Geometry convergence graphs improved and will now
display function value when cursor is over the graph point.
clicking in the graph will bring up the current point for
display
Tue Aug 10 Added support for reading Gamess/Gaussian/Mopac inputfiles
and Mopac/Ampac arc files.
Mon Aug 1 Added listbox to select orbitals, made internal rearrangements
for systematic handeling of queryboxes, listboxes
Some query boxes now remain on the screen untill a toggle
button is pressed
Mon Jul 11 Gamess/Gaussian frequencies/Norm. Modes can now be displayed.
Molden2.3:
Mon Jun 27 Improved shaded plotmode & switched to fully 3D controls
Tue May 17 Removed bugs on commandline parsing on some systems
Tue Feb 1 handle gaussian92 scf convergence
(turned on by #P in gaussian inputfile)
Jan 20 Made molden pc X compatible
Thu Dec 23 -c0.2 define depth of shading 0.0 is max, 1.0 is no shades
Tue Dec 16 removed bug in the H-bond on screen display routine
Wed Dec 15 -f with PDB files, forces connectivity to be build by molden
by default connectivity between amino acid atoms are read
from the PDB file and for all other atoms molden determines
the connectivity
Fri Dec 3 better handling hbond when more than one chain
better spheres, and beter coloring with shade
Thu Dec 2 Better atom selecting by cursor.
perspective is now uniform from large to small molecules
-p10.0 perspective flag
Tue Nov 30 Added reading of binary mopac/ampac *.gpt files
Fri Nov 26 -ofilename change the default plotfilename='plot'
trying to put in spheres with real depth, not satisf. yet
-d debug flag
Thu Nov 25 bug out of getmul.f, by Dirk Huckriede
Nov 10 Dec Alpha version, corrected problems in wrzmat.f
=========================================================================
TODO:
- improve zmat editor
- Density Functional orbitals of Gaussian94 ?
- Clean up handling of dummies
- Third rotation axis.
- Mopac IRC